# \#transcriptomics **URL:** https://help.galaxyproject.org/tag/transcriptomics/149.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Build expression matrix error](https://help.galaxyproject.org/t/build-expression-matrix-error/18553)
**Author:** [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\ **Replies:** 2\ **Last updated:** [October 30, 2026, 5:11am UTC](https://help.galaxyproject.org/t/build-expression-matrix-error/18553 "2026-10-30T05:11:44Z")
Hello I tried to run Build expression matrix with 2 abundance estimates files and salmon method, but got the following error message. Please help. Kamran Error, cmd: R --no-save --no-restore --no-site-file --no-init-… --- ## [Generate gene to transcript map](https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554)
**Author:** [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\ **Replies:** 1\ **Last updated:** [October 30, 2026, 4:44am UTC](https://help.galaxyproject.org/t/generate-gene-to-transcript-map/18554 "2026-10-30T04:44:44Z")
How does the ‘Generate gene to transcript map’ tool produces the file containing correspondence between gene ids and transcript ids based on the names of DE NOVO transcripts assembled by rnaSPAdes? The reference genome i… --- ## [DEseq2 error with salmon-quant input](https://help.galaxyproject.org/t/deseq2-error-with-salmon-quant-input/18559)
**Author:** [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\ **Replies:** 1\ **Last updated:** [October 29, 2026, 4:01pm UTC](https://help.galaxyproject.org/t/deseq2-error-with-salmon-quant-input/18559 "2026-10-29T16:01:12Z")
Dear All I ran DESeq2 and received following error message. I would appreciate help. Regards Kamran Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the … --- ## [Error in "Align reads and estimate abundance"](https://help.galaxyproject.org/t/error-in-align-reads-and-estimate-abundance/18480)
**Author:** [@kamran.azim](https://help.galaxyproject.org/u/kamran.azim)\ **Replies:** 2\ **Last updated:** [October 27, 2026, 5:01pm UTC](https://help.galaxyproject.org/t/error-in-align-reads-and-estimate-abundance/18480 "2026-10-27T17:01:07Z")
Hi Everyone I am getting the following error when running "Align reads and estimate abundance". Please help. Kamran Azim Error detected: Error, cmd: /usr/local/opt/trinity-2.15.1/util/support\_scripts/salmon\_trans\_to\_… --- ## [Trinity read normalization](https://help.galaxyproject.org/t/trinity-read-normalization/18527)
**Author:** [@analaura1202](https://help.galaxyproject.org/u/analaura1202)\ **Replies:** 1\ **Last updated:** [October 26, 2026, 4:37pm UTC](https://help.galaxyproject.org/t/trinity-read-normalization/18527 "2026-10-26T16:37:31Z")
Hello! I have a Trinity de novo assembly, and I would like to use the Trinity-normalized reads as input for rnaSPAdes so I can compare the two assemblies. Do you know how I could do this in Galaxy? Thanks! --- ## [Metatranscriptomic analysis fails to determine pathwasy with HUMAnN](https://help.galaxyproject.org/t/metatranscriptomic-analysis-fails-to-determine-pathwasy-with-humann/18426)
**Author:** [@jenny.gamezroessler](https://help.galaxyproject.org/u/jenny.gamezroessler)\ **Replies:** 3\ **Last updated:** [October 3, 2026, 12:29am UTC](https://help.galaxyproject.org/t/metatranscriptomic-analysis-fails-to-determine-pathwasy-with-humann/18426 "2026-10-03T00:29:48Z")
Hello Galaxy team, i write because i have a problem with the HUMAnN tool (v3.9 + galaxy1) i used on fecal NGS sequences (samples from four days). I have followed the tutorial “Metatranscriptomics analysis using microbio… --- ## [STARsolo custom reference fails during genomeGenerate — need genomeChrBinNbits for fragmented Nicotiana genome](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360)
**Author:** [@fforn](https://help.galaxyproject.org/u/fforn)\ **Replies:** 4\ **Last updated:** [September 3, 2026, 6:53pm UTC](https://help.galaxyproject.org/t/starsolo-custom-reference-fails-during-genomegenerate-need-genomechrbinnbits-for-fragmented-nicotiana-genome/18360 "2026-09-03T18:53:22Z")
Hi Galaxy Europe team, I am trying to reconstruct a published 10x Genomics v3 single-nucleus RNA-seq dataset from Nicotiana tabacum K326 using RNA STARsolo on singlecell.usegalaxy.eu. Tool: RNA STARsolo 2.7.11b+galaxy2 … --- ## [Immediate error when running RNA STAR](https://help.galaxyproject.org/t/immediate-error-when-running-rna-star/18319)
**Author:** [@knmcfarland](https://help.galaxyproject.org/u/knmcfarland)\ **Replies:** 2\ **Last updated:** [August 25, 2026, 3:31am UTC](https://help.galaxyproject.org/t/immediate-error-when-running-rna-star/18319 "2026-08-25T03:31:02Z")
Hi! I’m trying to align fastq files to the built in mouse genome (GRCm39/mm39) using RNA STAR. I am getting errors of “Encountered an unhandled exception while caching job destination dynamic rule” almost immediately or … --- ## [Featurecounts error with reference GTF file](https://help.galaxyproject.org/t/featurecounts-error-with-reference-gtf-file/18311)
**Author:** [@Xxl](https://help.galaxyproject.org/u/Xxl)\ **Replies:** 1\ **Last updated:** [August 24, 2026, 1:09am UTC](https://help.galaxyproject.org/t/featurecounts-error-with-reference-gtf-file/18311 "2026-08-24T01:09:58Z")
Hi, I’m troubleshooting an RNA-seq analysis in Galaxy and am running into an error at the featureCounts step. I am analyzing Xenopus laevis RNA-seq data and uploaded both the reference genome FASTA file and the correspo… --- ## [Notebooks: more about memory resources and HTP analysis](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267)
**Author:** [@0808](https://help.galaxyproject.org/u/0808)\ **Replies:** 2\ **Last updated:** [August 11, 2026, 7:31am UTC](https://help.galaxyproject.org/t/notebooks-more-about-memory-resources-and-htp-analysis/18267 "2026-08-11T07:31:33Z")
Title: Request for higher-memory resource for RSEM v1.3.1 due to OOM Hello Galaxy Europe Support Team, I am reprocessing the public PRJEB40416 gastric cancer RNA-seq dataset on usegalaxy.eu. STAR alignment has comple… --- ## [Stringtie help related to GTF file for zebrafish genome](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210)
**Author:** [@poojashukla](https://help.galaxyproject.org/u/poojashukla)\ **Replies:** 2\ **Last updated:** [July 28, 2026, 8:30pm UTC](https://help.galaxyproject.org/t/stringtie-help-related-to-gtf-file-for-zebrafish-genome/18210 "2026-07-28T20:30:55Z")
i want to know when i am doing stringtie and uploading GTF file of zebrafish genome its giving error or not matching notations with hisat2 in built genomic sequence, help me find zebrfish gemome GTF file that matches to … --- ## [lncRNA pipeline using GENCODE files](https://help.galaxyproject.org/t/lncrna-pipeline-using-gencode-files/18181)
**Author:** [@Ivan\_David\_Fonseca\_G](https://help.galaxyproject.org/u/Ivan_David_Fonseca_G)\ **Replies:** 2\ **Last updated:** [July 20, 2026, 4:27pm UTC](https://help.galaxyproject.org/t/lncrna-pipeline-using-gencode-files/18181 "2026-07-20T16:27:05Z")
Dear team, I’m seeking advice regarding an issue in my RNA‑seq analysis pipeline. My objective is to identify differentially expressed lncRNAs. The workflow I’m using includes fastp (trimming), HISAT2 (alignment), Strin… --- ## [ChiRa for Chimeric eClip data processing - Split ChiRa collapse out put as files to large processing](https://help.galaxyproject.org/t/chira-for-chimeric-eclip-data-processing-split-chira-collapse-out-put-as-files-to-large-processing/18097)
**Author:** [@S\_Staplet](https://help.galaxyproject.org/u/S_Staplet)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 3:08am UTC](https://help.galaxyproject.org/t/chira-for-chimeric-eclip-data-processing-split-chira-collapse-out-put-as-files-to-large-processing/18097 "2026-07-06T03:08:34Z")
Hi there, I’m using the ChiRA workflow from "RNA-RNA interactome data analysis" transcriptomics tutorial. And I have had to split my ChiRa collapse output files into 500k read fasta files to enable mapping; as the orig… --- ## [DEseq2: Interpreting 3 or more factor levels](https://help.galaxyproject.org/t/deseq2-interpreting-3-or-more-factor-levels/18133)
**Author:** [@tbd](https://help.galaxyproject.org/u/tbd)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 3:02am UTC](https://help.galaxyproject.org/t/deseq2-interpreting-3-or-more-factor-levels/18133 "2026-07-06T03:02:00Z")
Hello, I recently used DEseq2 to compare featureCounts output from 9 samples: 3 in each of 3 factor levels: Factor: Day Level 1: Day1 (samples 1, 2, 3) Level 2: Day2 (samples 4, 5, 6) Level 3 Day3 (samples 7, 8, 9) W… --- ## [How to set the reference level in DESeq2 for treatment vs control comparison?](https://help.galaxyproject.org/t/how-to-set-the-reference-level-in-deseq2-for-treatment-vs-control-comparison/18128)
**Author:** [@09303030076](https://help.galaxyproject.org/u/09303030076)\ **Replies:** 1\ **Last updated:** [July 6, 2026, 2:52am UTC](https://help.galaxyproject.org/t/how-to-set-the-reference-level-in-deseq2-for-treatment-vs-control-comparison/18128 "2026-07-06T02:52:56Z")
Hello, Dear I would like to ask whether the first factor in DESeq2 should be set as the control or the treatment when the goal is to evaluate the changes in the treatment compared to the control. --- ## [DESeq2 factors and factor level Input](https://help.galaxyproject.org/t/deseq2-factors-and-factor-level-input/17689)
**Author:** [@bveyb](https://help.galaxyproject.org/u/bveyb)\ **Replies:** 4\ **Last updated:** [May 5, 2026, 7:02am UTC](https://help.galaxyproject.org/t/deseq2-factors-and-factor-level-input/17689 "2026-05-05T07:02:35Z")
Dear Galaxy Support Team, if I’m running DESeq2 with a merged data collection containing 3 replicates (column) with group tags group:WT group:control, 3 replicates (column) with group tags group:hipp5 group:control, 3… --- ## [Issue with edgeR results for endometrial dataset](https://help.galaxyproject.org/t/issue-with-edger-results-for-endometrial-dataset/17631)
**Author:** [@Monish\_V](https://help.galaxyproject.org/u/Monish_V)\ **Replies:** 3\ **Last updated:** [April 30, 2026, 9:29pm UTC](https://help.galaxyproject.org/t/issue-with-edger-results-for-endometrial-dataset/17631 "2026-04-30T21:29:45Z")
Hi, I’m facing an issue while running edgeR on one of my datasets (endometrial samples). The same pipeline and settings worked correctly for my colorectal dataset, but for this one I’m consistently getting flat results … --- ## [Issue at RNA-STAR step: adjusting GTF annotation](https://help.galaxyproject.org/t/issue-at-rna-star-step-adjusting-gtf-annotation/17668)
**Author:** [@Sanjukta\_Ghosh](https://help.galaxyproject.org/u/Sanjukta_Ghosh)\ **Replies:** 3\ **Last updated:** [April 22, 2026, 4:56pm UTC](https://help.galaxyproject.org/t/issue-at-rna-star-step-adjusting-gtf-annotation/17668 "2026-04-22T16:56:34Z")
Hello Team, I am performing Refernce based RNA-Seq analysis, and I am stuck at the RNA STAR-based mapping step. After running with the following parameters, an error shows: An error occurred with this dataset. I am not … --- ## [Fatal error: using trinity](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218)
**Author:** [@guser](https://help.galaxyproject.org/u/guser)\ **Replies:** 2\ **Last updated:** [April 18, 2026, 2:32am UTC](https://help.galaxyproject.org/t/fatal-error-using-trinity/10218 "2026-04-18T02:32:45Z")
Hi I am using trinity and the error message is: "Fatal error: Exit code 1 () cp: -r not specified; omitting directory ‘trinity\_out\_dir/Trinity.tmp.fasta.salmon.idx’ /ocean/projects/mcb140028p/xcgalaxy/main/staging/50… --- ## [Error with de novo assembly using Trintiy](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563)
**Author:** [@Jose\_Manuel\_Latorre](https://help.galaxyproject.org/u/Jose_Manuel_Latorre)\ **Replies:** 5\ **Last updated:** [April 18, 2026, 2:28am UTC](https://help.galaxyproject.org/t/error-with-de-novo-assembly-using-trintiy/10563 "2026-04-18T02:28:46Z")
Dear Galaxy users, First, thanks in advance for your help, I am trying to get a de novo assembly from RNA-Seq data using Trintiy. I have just one sample that was sequenced in the Illumina platform with more or less 40 … --- ## [Improve genome annotation with RNA-Seq data](https://help.galaxyproject.org/t/improve-genome-annotation-with-rna-seq-data/6474)
**Author:** [@benjamin\_vdh](https://help.galaxyproject.org/u/benjamin_vdh)\ **Replies:** 1\ **Last updated:** [April 8, 2026, 1:45am UTC](https://help.galaxyproject.org/t/improve-genome-annotation-with-rna-seq-data/6474 "2026-04-08T01:45:52Z")
Hi there, I am currently working on RNA sequencing data from my model organism Volvox carteri for the first time. After checking the mapping in IGV i found that several reads map to regions in the genome, where no gene … --- ## [Custom PCA plot in Deseq2](https://help.galaxyproject.org/t/custom-pca-plot-in-deseq2/7433)
**Author:** [@Edling](https://help.galaxyproject.org/u/Edling)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 12:47am UTC](https://help.galaxyproject.org/t/custom-pca-plot-in-deseq2/7433 "2026-04-08T00:47:28Z")
Is there a way of obtaining the actual data tables used for plotting the PCA, MA etc plots that is part of the output when running DeSeq2? Thanks, Charlotte --- ## [cummeRbund tool tutorials guide](https://help.galaxyproject.org/t/cummerbund-tool-tutorials-guide/17626)
**Author:** [@Rachaita\_Mishra](https://help.galaxyproject.org/u/Rachaita_Mishra)\ **Replies:** 1\ **Last updated:** [April 6, 2026, 5:45pm UTC](https://help.galaxyproject.org/t/cummerbund-tool-tutorials-guide/17626 "2026-04-06T17:45:11Z")
what is the input format for this tools. The whole guide for this tool in Galaxy. --- ## [GoSeq GO analysis importing a gene categories file](https://help.galaxyproject.org/t/goseq-go-analysis-importing-a-gene-categories-file/17624)
**Author:** [@Alison](https://help.galaxyproject.org/u/Alison)\ **Replies:** 1\ **Last updated:** [April 1, 2026, 2:28pm UTC](https://help.galaxyproject.org/t/goseq-go-analysis-importing-a-gene-categories-file/17624 "2026-04-01T14:28:36Z")
I’m trying to run GOSeq on my data set of Arabidopsis thaliana transcripts. I have prepared the two input files for GoSeq as described in the hands on RNAseq tutorial, namely the Gene Ids and differential expression and … --- ## [Ouput unaligned reads into bam file with hisat2](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587)
**Author:** [@alixlem](https://help.galaxyproject.org/u/alixlem)\ **Replies:** 1\ **Last updated:** [March 18, 2026, 2:24pm UTC](https://help.galaxyproject.org/t/ouput-unaligned-reads-into-bam-file-with-hisat2/17587 "2026-03-18T14:24:49Z")
Hello, I have a list of genes and a list of RNAs. For each gene, I would like to know how many RNAs do not align. I am using hisat2 for alignments, and it gives me a fastaqsanger file with the unaligned reads, but the b… --- ## [EdgeR shows 0 dataset](https://help.galaxyproject.org/t/edger-shows-0-dataset/17519)
**Author:** [@Febri\_Gunawan](https://help.galaxyproject.org/u/Febri_Gunawan)\ **Replies:** 1\ **Last updated:** [March 1, 2026, 11:42pm UTC](https://help.galaxyproject.org/t/edger-shows-0-dataset/17519 "2026-03-01T23:42:25Z")
Hi, in these 2 days I am trying to run EdgeR from tximport output. It runs well, no error, but EdgeR gave me 0 dataset ouput! I am not sure what happened. I thought my tximport file problem, but I reran from my old data,… --- ## [Transcriptomics in Galaxy: Overview, Guides, Production Workflows](https://help.galaxyproject.org/t/transcriptomics-in-galaxy-overview-guides-production-workflows/17467)
**Author:** [@Gauravshree786](https://help.galaxyproject.org/u/Gauravshree786)\ **Replies:** 3\ **Last updated:** [February 18, 2026, 10:46pm UTC](https://help.galaxyproject.org/t/transcriptomics-in-galaxy-overview-guides-production-workflows/17467 "2026-02-18T22:46:17Z")
I have a paired end transcriptome dataset for plant and i want assembly of it but i have tried many time rnaSPAses is not working fine . Can any one help me with that --- ## [ChIP sequencing](https://help.galaxyproject.org/t/chip-sequencing/17461)
**Author:** [@Krishnendu\_Goswami](https://help.galaxyproject.org/u/Krishnendu_Goswami)\ **Replies:** 1\ **Last updated:** [February 16, 2026, 6:02pm UTC](https://help.galaxyproject.org/t/chip-sequencing/17461 "2026-02-16T18:02:34Z")
I am trying to analysis ChIP seq data . I got MultiQC, coverage from MACS2 (bigwig), bedtools annotatedbed on data. I hope i got everything, now i need to go for further step to find the the promoter region, but I am una… --- ## [Generating tx2gene map and filtering for rnaSPAdes (de novo)](https://help.galaxyproject.org/t/generating-tx2gene-map-and-filtering-for-rnaspades-de-novo/17380)
**Author:** [@Chamara\_Lakshitha](https://help.galaxyproject.org/u/Chamara_Lakshitha)\ **Replies:** 3\ **Last updated:** [January 31, 2026, 12:32am UTC](https://help.galaxyproject.org/t/generating-tx2gene-map-and-filtering-for-rnaspades-de-novo/17380 "2026-01-31T00:32:26Z")
I am performing de novo transcriptome analysis on a halophyte plant (no reference genome/GTF) using rnaSPAdes and Salmon. I need help with two specific steps in Galaxy: Gene-to-Transcript Map: How do I generate a tx2… --- ## [Gene and transcript level quant using salmon](https://help.galaxyproject.org/t/gene-and-transcript-level-quant-using-salmon/17117)
**Author:** [@aperreault](https://help.galaxyproject.org/u/aperreault)\ **Replies:** 4\ **Last updated:** [January 8, 2026, 11:40am UTC](https://help.galaxyproject.org/t/gene-and-transcript-level-quant-using-salmon/17117 "2026-01-08T11:40:19Z")
Hi all! I’m trying to use Salmon quant to get gene and transcript level quantification. Below are the settings I’m using: Salmon quant (Galaxy Version 1.10.1+galaxy4) “reads” mode Using built-in hg38 transcriptome pair… [Next page](https://help.galaxyproject.org/tag/transcriptomics/149.md?match_all_tags=true&page=1&tags%5B%5D=transcriptomics)