# Resources **URL:** https://help.galaxyproject.org/c/resources/14.md?page=1 [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) **Page:** 2 --- ## [How to analyze trimmed reads by Shovill Faster Spades Assembly tool](https://help.galaxyproject.org/t/how-to-analyze-trimmed-reads-by-shovill-faster-spades-assembly-tool/13790)
**Author:** [@huiping](https://help.galaxyproject.org/u/huiping)\ **Replies:** 2\ **Last updated:** [October 31, 2024, 8:31am UTC](https://help.galaxyproject.org/t/how-to-analyze-trimmed-reads-by-shovill-faster-spades-assembly-tool/13790 "2024-10-31T08:31:32Z")
Hi, I used your Timmomatic tool to trim my reads and obtained 4 files: fastq R1 paired, fastq R2 paired, fastq R1 unpaired and fastq R2 unpaired. Can I use Collapse Collection tool to get a single dataset, then use Shovi… --- ## [FAQ: NCBI reference data](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720)
**Author:** [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Replies:** 0\ **Last updated:** [June 12, 2025, 8:36pm UTC](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720 "2025-06-12T20:36:23Z")
:speech\_balloon: How to find NCBI Reference data? Q: Where can I find the URL links to a reference genome FASTA, annotation, or GenBank file? A: Use the NCBI Genome Assembly page for the organism of interest — for examp… --- ## [Assembly statistics in reference based RNA seq analysis\_tools](https://help.galaxyproject.org/t/assembly-statistics-in-reference-based-rna-seq-analysis-tools/10741)
**Author:** [@susheel\_raina](https://help.galaxyproject.org/u/susheel_raina)\ **Replies:** 1\ **Last updated:** [September 6, 2023, 5:34pm UTC](https://help.galaxyproject.org/t/assembly-statistics-in-reference-based-rna-seq-analysis-tools/10741 "2023-09-06T17:34:20Z")
How to estimate the assembly stats in reference based RNA seq analysis? I used FastQ-Trimmomatic-HISAT2-Stringtie-Stringtie merge-Deseq2 pipeline for analysis of my RNA seq data. Which tools in galaxy should I use to e… --- ## [How to review a BAM! Metadata, reference genome, workflows](https://help.galaxyproject.org/t/how-to-review-a-bam-metadata-reference-genome-workflows/14000)
**Author:** [@Sina](https://help.galaxyproject.org/u/Sina)\ **Replies:** 1\ **Last updated:** [November 27, 2024, 6:17pm UTC](https://help.galaxyproject.org/t/how-to-review-a-bam-metadata-reference-genome-workflows/14000 "2024-11-27T18:17:46Z")
Hello I was working on a dataset, unfortunately during the analysis phase with Infer exprement my data became unknown and for this reason I cannot perform the multiQC operation, can you help me in this regard?!! --- ## [Help with RNA Star, Featurecounts, and reference annotation choices](https://help.galaxyproject.org/t/help-with-rna-star-featurecounts-and-reference-annotation-choices/16190)
**Author:** [@nmozdoori](https://help.galaxyproject.org/u/nmozdoori)\ **Replies:** 1\ **Last updated:** [August 19, 2025, 6:47pm UTC](https://help.galaxyproject.org/t/help-with-rna-star-featurecounts-and-reference-annotation-choices/16190 "2025-08-19T18:47:16Z")
I’m performing a meta-analysis across multiple human RNA-seq datasets. Given that my STAR alignment rate is \>70% but featureCounts assigns \<50% with many ‘no feature’ reads , I am confident about the strandness setting, … --- ## [Cut and run: MACS2 error](https://help.galaxyproject.org/t/cut-and-run-macs2-error/15808)
**Author:** [@bezinka](https://help.galaxyproject.org/u/bezinka)\ **Replies:** 6\ **Last updated:** [July 9, 2025, 12:39am UTC](https://help.galaxyproject.org/t/cut-and-run-macs2-error/15808 "2025-07-09T00:39:11Z")
Hi, I would like to ask for help with MACS2. I follow tutorial Epigenetics: CUT&RUN data analysis and I have problem with MACS2 tool. I tried to check: files are not empty, format of the file should be fine (I did singl… --- ## [HUMAnN fails due to MetaPhlAn database mismatch](https://help.galaxyproject.org/t/humann-fails-due-to-metaphlan-database-mismatch/16501)
**Author:** [@sri\_microbiome](https://help.galaxyproject.org/u/sri_microbiome)\ **Replies:** 1\ **Last updated:** [November 17, 2025, 8:29pm UTC](https://help.galaxyproject.org/t/humann-fails-due-to-metaphlan-database-mismatch/16501 "2025-11-17T20:29:14Z")
Hello Galaxy team, I am trying to run HUMAnN (v3.7 / v3.9) on usegalaxy.eu for human fecal shotgun metagenomic reads.- just 2 samples , I converted fastq to fasta as well even then the error continued as I looked deeper… --- ## [Linking mouse gene IDs/name to Encode IDs following Salmon and DESeq analysis](https://help.galaxyproject.org/t/linking-mouse-gene-ids-name-to-encode-ids-following-salmon-and-deseq-analysis/15225)
**Author:** [@lucasdsouza](https://help.galaxyproject.org/u/lucasdsouza)\ **Replies:** 2\ **Last updated:** [April 16, 2025, 3:45pm UTC](https://help.galaxyproject.org/t/linking-mouse-gene-ids-name-to-encode-ids-following-salmon-and-deseq-analysis/15225 "2025-04-16T15:45:59Z")
Hi all, I’m running into an unusual problem when analyzing mouse RNA data on Galaxy. After I upload the R1 and R2 files for my samples, I first analyze for counts using Salmon against the transcripts reference file down… --- ## [Need help with the dataset error report on MITOS (version 1.1.7) de-novo annotation tool of metazoan mitochondrial genomes](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474)
**Author:** [@gerry\_ramos\_jr](https://help.galaxyproject.org/u/gerry_ramos_jr)\ **Replies:** 5\ **Last updated:** [September 24, 2024, 11:03pm UTC](https://help.galaxyproject.org/t/need-help-with-the-dataset-error-report-on-mitos-version-1-1-7-de-novo-annotation-tool-of-metazoan-mitochondrial-genomes/13474 "2024-09-24T23:03:58Z")
An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/mitos/mitos/1.1.7+galaxy0. Execution resulted in “Fatal error: Exit code 1 ()” message. Tool generated the following standard error: Traceback … --- ## [TEtranscripts input datasets](https://help.galaxyproject.org/t/tetranscripts-input-datasets/16131)
**Author:** [@ducbiologygroup](https://help.galaxyproject.org/u/ducbiologygroup)\ **Replies:** 3\ **Last updated:** [August 11, 2025, 6:48pm UTC](https://help.galaxyproject.org/t/tetranscripts-input-datasets/16131 "2025-08-11T18:48:00Z")
I want to run TEtranscripts between treated and control groups. Each group has 3 technical replicates in data collection. However, when I set two collections (one for treated and one for control) for TEtranscripts, it is… --- ## [Ensembl gene annotation gtf for rat problem with RNA STAR](https://help.galaxyproject.org/t/ensembl-gene-annotation-gtf-for-rat-problem-with-rna-star/14818)
**Author:** [@ed\_bahnson](https://help.galaxyproject.org/u/ed_bahnson)\ **Replies:** 2\ **Last updated:** [February 26, 2025, 1:54pm UTC](https://help.galaxyproject.org/t/ensembl-gene-annotation-gtf-for-rat-problem-with-rna-star/14818 "2025-02-26T13:54:10Z")
Hi I am trying to map using RNA star. I used the built-in rat genome rn6 and I downloaded the annotation gtf from ensembl and when running STAR I got an error:“no valid exon lines in the GTF file.” I removed the header … --- ## [CREx\_rearrangement scenario](https://help.galaxyproject.org/t/crex-rearrangement-scenario/15918)
**Author:** [@yaoyuan](https://help.galaxyproject.org/u/yaoyuan)\ **Replies:** 4\ **Last updated:** [September 4, 2025, 9:18am UTC](https://help.galaxyproject.org/t/crex-rearrangement-scenario/15918 "2025-09-04T09:18:42Z")
I want to know how to use Galaxy to generate a “rearrangement scenario”? Like Figure 1 in the paper “doi:10.1093/bioinformatics/btm468” when CREx was released, or in the instructions in the old version of the CREx inter… --- ## [How can I rename a paired Fastq file?](https://help.galaxyproject.org/t/how-can-i-rename-a-paired-fastq-file/15784)
**Author:** [@Caroline\_R](https://help.galaxyproject.org/u/Caroline_R)\ **Replies:** 4\ **Last updated:** [June 24, 2025, 9:24pm UTC](https://help.galaxyproject.org/t/how-can-i-rename-a-paired-fastq-file/15784 "2025-06-24T21:24:54Z")
I am following along with the Reference-based RNA-Seq tutorial, but I am having an issue where, when I go to rename the paired fastqs, it doesn’t work. This is what I see: Then I type in my new file name: Then I… --- ## [Kraken2 reference database for shotgun sequencing data](https://help.galaxyproject.org/t/kraken2-reference-database-for-shotgun-sequencing-data/16319)
**Author:** [@bgood07](https://help.galaxyproject.org/u/bgood07)\ **Replies:** 4\ **Last updated:** [September 30, 2025, 9:38pm UTC](https://help.galaxyproject.org/t/kraken2-reference-database-for-shotgun-sequencing-data/16319 "2025-09-30T21:38:12Z")
Hello, I am using the GalaxyEu server and working on analyzing some shotgun sequencing data from soil, produce, and manure amendment samples. I am using Kraken2 for the taxonomic classification. What reference databases … --- ## [Why collections?](https://help.galaxyproject.org/t/why-collections/16411)
**Author:** [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Replies:** 0\ **Last updated:** [October 21, 2025, 10:41pm UTC](https://help.galaxyproject.org/t/why-collections/16411 "2025-10-21T22:41:50Z")
Collections are one of the super-killer features of Galaxy! By Anton Nekrutenko October 21, 2025 --- ## [Tool 'sra\_source' does not exist](https://help.galaxyproject.org/t/tool-sra-source-does-not-exist/16274)
**Author:** [@Atefeh\_Bahmei](https://help.galaxyproject.org/u/Atefeh_Bahmei)\ **Replies:** 2\ **Last updated:** [September 23, 2025, 6:52pm UTC](https://help.galaxyproject.org/t/tool-sra-source-does-not-exist/16274 "2025-09-23T18:52:48Z")
Hi my friends. I have a paired-end data (PRJNA998059) I wanna analyze it with GALAXY. However, when I wanna deliver it from GEO NCBI site to galaxy I get this error “Tool ‘sra\_source’ does not exist.” Is there any soluti… --- ## [How database assignments are used to access a fasta index: custom genomes, custom builds, server indexes](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225)
**Author:** [@Choute](https://help.galaxyproject.org/u/Choute)\ **Replies:** 1\ **Last updated:** [April 17, 2024, 6:35pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225 "2024-04-17T18:35:32Z")
I’m currently encountering some issues while running a dataset through the Qualimap BamQC tool. Specifically, I’m receiving the following errors: Fatal error: Exit code 1 Input mapping file not found Has anyone experi… --- ## [Data Storage choices when using Workflows](https://help.galaxyproject.org/t/data-storage-choices-when-using-workflows/14372)
**Author:** [@Lee\_Wonsik](https://help.galaxyproject.org/u/Lee_Wonsik)\ **Replies:** 2\ **Last updated:** [January 10, 2025, 3:06am UTC](https://help.galaxyproject.org/t/data-storage-choices-when-using-workflows/14372 "2025-01-10T03:06:56Z")
Hi, I uploaded my files to the 30-day storage and ran my workflow. However, I noticed that several result files were deposited into the permanent storage. Why did this happen, and how can I fix this issue? --- ## [Archived history](https://help.galaxyproject.org/t/archived-history/15096)
**Author:** [@cjain](https://help.galaxyproject.org/u/cjain)\ **Replies:** 3\ **Last updated:** [April 1, 2025, 6:22pm UTC](https://help.galaxyproject.org/t/archived-history/15096 "2025-04-01T18:22:37Z")
I accidentally archived one of my histories and have not been able to find out how to un-archive it. Could somebody point me in the right direction? Thanks! --- ## [Collection folder VIDEO: How to create a single or paired end dataset collection folder (shapes and organization)](https://help.galaxyproject.org/t/collection-folder-video-how-to-create-a-single-or-paired-end-dataset-collection-folder-shapes-and-organization/16296)
**Author:** [@Bioinfoufgd](https://help.galaxyproject.org/u/Bioinfoufgd)\ **Replies:** 3\ **Last updated:** [September 29, 2025, 7:27pm UTC](https://help.galaxyproject.org/t/collection-folder-video-how-to-create-a-single-or-paired-end-dataset-collection-folder-shapes-and-organization/16296 "2025-09-29T19:27:56Z")
I need help. I’m trying to use Metawrap on usegalaxy.eu to analyze binning files. After entering the binning files, it asks for the original files prior to the assembly. This is required information, but there’s no optio… --- ## [Resolving memory failures with SPAdes](https://help.galaxyproject.org/t/resolving-memory-failures-with-spades/13322)
**Author:** [@David\_Read](https://help.galaxyproject.org/u/David_Read)\ **Replies:** 1\ **Last updated:** [August 27, 2024, 5:30pm UTC](https://help.galaxyproject.org/t/resolving-memory-failures-with-spades/13322 "2024-08-27T17:30:29Z")
Hi everyone. What is the maximum number of paired-end reads that can be used as an input for a SPAdes assembly to avoid getting a “dataset too large” error? Thanks! --- ## [Inquiry about lettuce genome](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608)
**Author:** [@Kelvin](https://help.galaxyproject.org/u/Kelvin)\ **Replies:** 2\ **Last updated:** [October 7, 2024, 5:20pm UTC](https://help.galaxyproject.org/t/inquiry-about-lettuce-genome/13608 "2024-10-07T17:20:58Z")
Hello, I want to ask if galaxy has lettuce reference genome. I’m considering using galaxy for my RNA-seq project in lettuce. Thank you --- ## [Question about UMI-tools extract: different version from the tutorial?](https://help.galaxyproject.org/t/question-about-umi-tools-extract-different-version-from-the-tutorial/15654)
**Author:** [@lotus](https://help.galaxyproject.org/u/lotus)\ **Replies:** 3\ **Last updated:** [August 13, 2025, 8:02am UTC](https://help.galaxyproject.org/t/question-about-umi-tools-extract-different-version-from-the-tutorial/15654 "2025-08-13T08:02:01Z")
I am learning the tutorial of Pre-processing of Single-Cell RNA Data the UMI-tools extract on the tutorial is Galaxy version 0.5.5.1 but the current version is Galaxy Version 1.1.6+galaxy0. The following parameters are … --- ## [Active (green) History dataset: unable to use as input as tools say it was deleted](https://help.galaxyproject.org/t/active-green-history-dataset-unable-to-use-as-input-as-tools-say-it-was-deleted/14197)
**Author:** [@Laura\_Peirson](https://help.galaxyproject.org/u/Laura_Peirson)\ **Replies:** 3\ **Last updated:** [December 17, 2024, 8:20pm UTC](https://help.galaxyproject.org/t/active-green-history-dataset-unable-to-use-as-input-as-tools-say-it-was-deleted/14197 "2024-12-17T20:20:17Z")
I did some cleaning of my histories recently and deleted and purged several items/histories so I could run new tools. I did not delete a dataset containing a list with 302 fastqsanger.gz pairs. The dataset is green. I ca… --- ## [Downloading a List with 250+ files and Renaming](https://help.galaxyproject.org/t/downloading-a-list-with-250-files-and-renaming/15359)
**Author:** [@zpho3nix](https://help.galaxyproject.org/u/zpho3nix)\ **Replies:** 2\ **Last updated:** [May 6, 2025, 10:18pm UTC](https://help.galaxyproject.org/t/downloading-a-list-with-250-files-and-renaming/15359 "2025-05-06T22:18:54Z")
Hi, so I’ve completed my analysis in Galaxy and now when I try to download a list it never initiates. I can download the individual files, but when one has over 700 results to download individual files can be rather tedi… --- ## [Extract Genomic DNA](https://help.galaxyproject.org/t/extract-genomic-dna/12909)
**Author:** [@Maria\_F](https://help.galaxyproject.org/u/Maria_F)\ **Replies:** 1\ **Last updated:** [July 9, 2024, 6:07pm UTC](https://help.galaxyproject.org/t/extract-genomic-dna/12909 "2024-07-09T18:07:30Z")
I’m using the Extract Genomic DNA tool on usegalaxy.org. I need to choose the source for the reference genome, and if I select a locally cached, no options show up. My input database file is associated with the reference… --- ## [How do I use galaxy tools to create a paired end collection folder (data shapes and organization)](https://help.galaxyproject.org/t/how-do-i-use-galaxy-tools-to-create-a-paired-end-collection-folder-data-shapes-and-organization/14032)
**Author:** [@HGM](https://help.galaxyproject.org/u/HGM)\ **Replies:** 2\ **Last updated:** [December 3, 2024, 4:50am UTC](https://help.galaxyproject.org/t/how-do-i-use-galaxy-tools-to-create-a-paired-end-collection-folder-data-shapes-and-organization/14032 "2024-12-03T04:50:48Z")
How do I use galaxy tools to concatenate paired end data and create a collection for furher analysis --- ## [Panaroo tool help](https://help.galaxyproject.org/t/panaroo-tool-help/15228)
**Author:** [@kavya23247](https://help.galaxyproject.org/u/kavya23247)\ **Replies:** 1\ **Last updated:** [April 16, 2025, 10:39pm UTC](https://help.galaxyproject.org/t/panaroo-tool-help/15228 "2025-04-16T22:39:24Z")
I have prokka-annotated files of different Metagenome Assembled Genomes. Can I use panaroo for pangenome analysis. One more question is that What kind of output plot does panaroo generates. --- ## [Need help to run Phyloseq in Galaxy to characterize microbial taxa](https://help.galaxyproject.org/t/need-help-to-run-phyloseq-in-galaxy-to-characterize-microbial-taxa/13423)
**Author:** [@Winnifred](https://help.galaxyproject.org/u/Winnifred)\ **Replies:** 2\ **Last updated:** [September 17, 2024, 4:36am UTC](https://help.galaxyproject.org/t/need-help-to-run-phyloseq-in-galaxy-to-characterize-microbial-taxa/13423 "2024-09-17T04:36:15Z")
I am trying to run phyloseq to charactize microbial community of plant sample. I used QIIME2 to generate barplots. I downloaded barplot as a csv file. I am trying to use phyloseq in Galaxy Europe to generate microbial pr… --- ## [An error of limma](https://help.galaxyproject.org/t/an-error-of-limma/12389)
**Author:** [@XIANG\_CHI](https://help.galaxyproject.org/u/XIANG_CHI)\ **Replies:** 1\ **Last updated:** [May 2, 2024, 8:20pm UTC](https://help.galaxyproject.org/t/an-error-of-limma/12389 "2024-05-02T20:20:16Z")
Hello there, I am trying to generate some DE tables using RNA-Seq data in Limma but I am getting this error message: Warning message: In Sys.setlocale(“LC\_MESSAGES”, “en\_US.UTF-8”) : OS reports request to set locale t… --- ## [Error with Visualize with Krona tool? Use Krona Pie Chart instead!](https://help.galaxyproject.org/t/error-with-visualize-with-krona-tool-use-krona-pie-chart-instead/14562)
**Author:** [@gajendrajoshi](https://help.galaxyproject.org/u/gajendrajoshi)\ **Replies:** 1\ **Last updated:** [January 28, 2025, 2:11am UTC](https://help.galaxyproject.org/t/error-with-visualize-with-krona-tool-use-krona-pie-chart-instead/14562 "2025-01-28T02:11:22Z")
Error on bug report page is cannot execute: required file not found I am trying to visualize with Krona based on the output file of the Krona pie chart from the taxonomic profile. The visualization with the Krona tool … --- ## [MITOS2 error can't run job](https://help.galaxyproject.org/t/mitos2-error-cant-run-job/16174)
**Author:** [@bioinfokg](https://help.galaxyproject.org/u/bioinfokg)\ **Replies:** 3\ **Last updated:** [August 29, 2025, 6:27pm UTC](https://help.galaxyproject.org/t/mitos2-error-cant-run-job/16174 "2025-08-29T18:27:48Z")
Hi, I’ve tried to use MITOS2 tool, and the following error seems to persist: The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error … --- ## [Help me with the error on mem bwa](https://help.galaxyproject.org/t/help-me-with-the-error-on-mem-bwa/13675)
**Author:** [@krupa\_natrajan](https://help.galaxyproject.org/u/krupa_natrajan)\ **Replies:** 1\ **Last updated:** [October 15, 2024, 7:17pm UTC](https://help.galaxyproject.org/t/help-me-with-the-error-on-mem-bwa/13675 "2024-10-15T19:17:49Z")
I am new to gelaxy. help me with this error \[mem\_sam\_pe\] paired reads have different names: “LH00271:14:22CCGHLT3:4:1101:27028:1080”, “LH00271:14:22CCGHLT3:4:1101:25308:1080” --- ## [Using LotuS2: tutorials and resources](https://help.galaxyproject.org/t/using-lotus2-tutorials-and-resources/16133)
**Author:** [@hyungz](https://help.galaxyproject.org/u/hyungz)\ **Replies:** 3\ **Last updated:** [August 12, 2025, 6:22pm UTC](https://help.galaxyproject.org/t/using-lotus2-tutorials-and-resources/16133 "2025-08-12T18:22:10Z")
Hi, everyone, The original LotuS2 has a option whether paired reads are merged before or after clustering (https://lotus2.earlham.ac.uk/main.php?site=downloads). But I can not find such a option in the LotuS2 on Galaxy… --- ## [Asking about qiime2 tools import](https://help.galaxyproject.org/t/asking-about-qiime2-tools-import/15795)
**Author:** [@Gehad\_Abdelsattar\_Mo](https://help.galaxyproject.org/u/Gehad_Abdelsattar_Mo)\ **Replies:** 1\ **Last updated:** [August 5, 2025, 6:39pm UTC](https://help.galaxyproject.org/t/asking-about-qiime2-tools-import/15795 "2025-08-05T18:39:36Z")
Hello, I have multiplexed 16S rRNA paired-end data. When I tried to import the dataset as qiime2 artifact using (EMPPairedEndSequences) it gave me an error. --- ## [Kraken2 Not supporting the required formats for paired sequencing](https://help.galaxyproject.org/t/kraken2-not-supporting-the-required-formats-for-paired-sequencing/16245)
**Author:** [@raptor\_007](https://help.galaxyproject.org/u/raptor_007)\ **Replies:** 1\ **Last updated:** [September 8, 2025, 8:08pm UTC](https://help.galaxyproject.org/t/kraken2-not-supporting-the-required-formats-for-paired-sequencing/16245 "2025-09-08T20:08:30Z")
Hi, I have a set of paired-end samples generated from the Illumina platform. I’ve been trying to run Kraken2 on them using the Galaxy Europe server with the suggested formats. However, I noticed that paired-end input doe… --- ## [This job was terminated because itused more memory than it wasallocated](https://help.galaxyproject.org/t/this-job-was-terminated-because-itused-more-memory-than-it-wasallocated/15297)
**Author:** [@1263201095](https://help.galaxyproject.org/u/1263201095)\ **Replies:** 1\ **Last updated:** [April 25, 2025, 4:40pm UTC](https://help.galaxyproject.org/t/this-job-was-terminated-because-itused-more-memory-than-it-wasallocated/15297 "2025-04-25T16:40:12Z")
I used the tool ‘Scanpy FilterCells’, but the result showed that it exceeded memory. However, I believe the number of cells is not that large, as shown in the image below. How could this issue occur? Thank you! --- ## [Need Help with Mapping Genome Skimming Data and Generating Consensus Sequences in Galaxy](https://help.galaxyproject.org/t/need-help-with-mapping-genome-skimming-data-and-generating-consensus-sequences-in-galaxy/13447)
**Author:** [@guillermo\_sr24](https://help.galaxyproject.org/u/guillermo_sr24)\ **Replies:** 1\ **Last updated:** [September 16, 2024, 7:16pm UTC](https://help.galaxyproject.org/t/need-help-with-mapping-genome-skimming-data-and-generating-consensus-sequences-in-galaxy/13447 "2024-09-16T19:16:42Z")
Hello everyone, I’m relatively new to genomic data management and am learning as I go. I have some Genome Skimming data and I’d like to map it to a concatenated gene sequence (from the HybSeq probes of GoFlag). Doing th… --- ## [Error reported for fgsea - gene set enrichment tool](https://help.galaxyproject.org/t/error-reported-for-fgsea-gene-set-enrichment-tool/15431)
**Author:** [@pacthoen](https://help.galaxyproject.org/u/pacthoen)\ **Replies:** 1\ **Last updated:** [May 16, 2025, 6:51pm UTC](https://help.galaxyproject.org/t/error-reported-for-fgsea-gene-set-enrichment-tool/15431 "2025-05-16T18:51:07Z")
Hi I am using fgsea for Gene Set Enrichment Analysis on mouse data. As input a tabular file with column1 containing gene symbols, column2 containing LogFC sorted in descending order. I tried both with gmt file and wit… --- ## [About DESeq2 Errors](https://help.galaxyproject.org/t/about-deseq2-errors/13229)
**Author:** [@Mina](https://help.galaxyproject.org/u/Mina)\ **Replies:** 1\ **Last updated:** [August 14, 2024, 10:00pm UTC](https://help.galaxyproject.org/t/about-deseq2-errors/13229 "2024-08-14T22:00:32Z")
Hi, I am trying to perform a gene expression analysis of a FeatureCounts file using the DESeq2 tool. I have no problem up to FeatureCounts, but when I do DESeq, which file should I use for ‘Factor level’ → ‘Count file’… --- ## [Apollo help for Create or Update Organism](https://help.galaxyproject.org/t/apollo-help-for-create-or-update-organism/15021)
**Author:** [@hhossei](https://help.galaxyproject.org/u/hhossei)\ **Replies:** 1\ **Last updated:** [March 17, 2025, 5:52pm UTC](https://help.galaxyproject.org/t/apollo-help-for-create-or-update-organism/15021 "2025-03-17T17:52:09Z")
Server: UseGalaxy.eu Tutorial: Refining Genome Annotations with Apollo (prokaryotes) Step: Create or Update Organism Error: “Fatal error: Exit code 1” with “Exception: Unexpected response from apollo 504” Details: Apoll… --- ## [2025 Update! Convert Genome Coordinates? Avoid ⚠ Liftover and try using CrossMap](https://help.galaxyproject.org/t/2025-update-convert-genome-coordinates-avoid-liftover-and-try-using-crossmap/13418)
**Author:** [@Priyanka\_Roy1](https://help.galaxyproject.org/u/Priyanka_Roy1)\ **Replies:** 1\ **Last updated:** [September 12, 2024, 6:00pm UTC](https://help.galaxyproject.org/t/2025-update-convert-genome-coordinates-avoid-liftover-and-try-using-crossmap/13418 "2024-09-12T18:00:04Z")
I WANT TO USE LIFT OVER ANNOTATION FOR Pv Sal 1 version 63 TO PvP01 version 63. I am unable to do so,as the options are not available. Please help me with the same. --- ## [Kraken2 Job Fails Repeatedly on Galaxy](https://help.galaxyproject.org/t/kraken2-job-fails-repeatedly-on-galaxy/16067)
**Author:** [@Abdul\_Latif\_shamozai](https://help.galaxyproject.org/u/Abdul_Latif_shamozai)\ **Replies:** 2\ **Last updated:** [July 30, 2025, 4:56pm UTC](https://help.galaxyproject.org/t/kraken2-job-fails-repeatedly-on-galaxy/16067 "2025-07-30T16:56:25Z")
I’m trying to run Kraken2 on Galaxy Europe, but the job fails every time—looking for help to identify and fix the issue. --- ## [Convert GTF to BED12](https://help.galaxyproject.org/t/convert-gtf-to-bed12/16221)
**Author:** [@Atefeh\_Bahmei](https://help.galaxyproject.org/u/Atefeh_Bahmei)\ **Replies:** 1\ **Last updated:** [August 28, 2025, 11:28pm UTC](https://help.galaxyproject.org/t/convert-gtf-to-bed12/16221 "2025-08-28T23:28:15Z")
For mapping I down loded GTF3.GZ file and I ad no problem when I wanted to run mapping,however for converting this file to bed file the uncompressed one cant not be uploded. what could I do --- ## [MaAsLin2 job fails due to glmmTMB / TMB version mismatch](https://help.galaxyproject.org/t/maaslin2-job-fails-due-to-glmmtmb-tmb-version-mismatch/16205)
**Author:** [@v20024](https://help.galaxyproject.org/u/v20024)\ **Replies:** 2\ **Last updated:** [August 21, 2025, 6:34pm UTC](https://help.galaxyproject.org/t/maaslin2-job-fails-due-to-glmmtmb-tmb-version-mismatch/16205 "2025-08-21T18:34:42Z")
Hello Galaxy Team, I have been trying to run MaAsLin2 on usegalaxy.eu, but the job consistently fails after some time. The error log shows the following messages: Error: glmmTMB models require glmmTMB \>= 1.1.8 Install… --- ## [Large genome assembly? See VGP resources and access your self-serve extended data storage!](https://help.galaxyproject.org/t/large-genome-assembly-see-vgp-resources-and-access-your-self-serve-extended-data-storage/16194)
**Author:** [@Mokammel\_Hossain](https://help.galaxyproject.org/u/Mokammel_Hossain)\ **Replies:** 1\ **Last updated:** [August 20, 2025, 5:07pm UTC](https://help.galaxyproject.org/t/large-genome-assembly-see-vgp-resources-and-access-your-self-serve-extended-data-storage/16194 "2025-08-20T17:07:30Z")
After doing illumina sequencing, I have found forward (121.5 gb) and reverse (121.5 gb) fastq files of Fasciola gigantica. I want to do assembly using galaxy. Is it possible for this large size data? If yes, please tell … --- ## [DADA2 Merge Pairs troubleshooting](https://help.galaxyproject.org/t/dada2-merge-pairs-troubleshooting/16215)
**Author:** [@karenandreac](https://help.galaxyproject.org/u/karenandreac)\ **Replies:** 1\ **Last updated:** [August 27, 2025, 4:10pm UTC](https://help.galaxyproject.org/t/dada2-merge-pairs-troubleshooting/16215 "2025-08-27T16:10:12Z")
Hello! I’m using DADA2 in galaxy France. When I ran the tool Merge Pairs, I had an error saying that the files from dada and deRep do not correspond. I tried to check the order of the files to see if the match, but the … --- ## [How to inspect the details of a tool wrapper: reproducibility and versioning](https://help.galaxyproject.org/t/how-to-inspect-the-details-of-a-tool-wrapper-reproducibility-and-versioning/13416)
**Author:** [@asma\_ivazeh](https://help.galaxyproject.org/u/asma_ivazeh)\ **Replies:** 1\ **Last updated:** [September 11, 2024, 5:11pm UTC](https://help.galaxyproject.org/t/how-to-inspect-the-details-of-a-tool-wrapper-reproducibility-and-versioning/13416 "2024-09-11T17:11:10Z")
Dear Galaxy Admins, I hope this message finds you well. I am currently working on a project that requires the use of the sam\_to\_bam tool, specifically version 2.1.1, from the following ToolShed repository: bash Copy c… --- ## [Flye giving error with bacterial genome](https://help.galaxyproject.org/t/flye-giving-error-with-bacterial-genome/16203)
**Author:** [@lcn](https://help.galaxyproject.org/u/lcn)\ **Replies:** 1\ **Last updated:** [August 21, 2025, 4:33pm UTC](https://help.galaxyproject.org/t/flye-giving-error-with-bacterial-genome/16203 "2025-08-21T16:33:17Z")
Hello community, I was trying to assemble a bacterial genome of about 2.1 Mb using flye. These are long reads produced with nanopore that I decompressed and then filtered by length; I have used this protocol several ti… --- ## [SnpSift Filter help](https://help.galaxyproject.org/t/snpsift-filter-help/14308)
**Author:** [@m2405398](https://help.galaxyproject.org/u/m2405398)\ **Replies:** 1\ **Last updated:** [January 3, 2025, 6:46pm UTC](https://help.galaxyproject.org/t/snpsift-filter-help/14308 "2025-01-03T18:46:26Z")
can someone help me on understanding how to use this filter? Tried 50 different commands but none workx [Previous page](https://help.galaxyproject.org/c/resources/14.md?per_page=50) [Next page](https://help.galaxyproject.org/c/resources/14.md?page=2&per_page=50)