# \#rna-seq **URL:** https://help.galaxyproject.org/tag/rna-seq/400.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [I can't run EGSEA on DEGs generated by limma-voom](https://help.galaxyproject.org/t/i-cant-run-egsea-on-degs-generated-by-limma-voom/18213)
**Author:** [@bahar125d](https://help.galaxyproject.org/u/bahar125d)\ **Replies:** 1\ **Last updated:** [July 27, 2026, 11:27pm UTC](https://help.galaxyproject.org/t/i-cant-run-egsea-on-degs-generated-by-limma-voom/18213 "2026-07-27T23:27:25Z")
Hello, I am trying to run EGSEA un Galaxy. I already have my list of differentially expressed genes, run by Limma-Voom. I have 6 samples in total, 3 controls and 3 treated ones. According to the step-by-step tutorial on… --- ## [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 … --- ## [How to extract count matrix from BAM files of scRNA-seq experiment in Galaxy Server?](https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207)
**Author:** [@mdka00001](https://help.galaxyproject.org/u/mdka00001)\ **Replies:** 1\ **Last updated:** [April 10, 2025, 12:48pm UTC](https://help.galaxyproject.org/t/how-to-extract-count-matrix-from-bam-files-of-scrna-seq-experiment-in-galaxy-server/15207 "2025-04-10T12:48:50Z")
I am trying to work on a public experimental scRNA-seq dataset of 12 samples. These samples are pooled with 10x Chromium. I have the SRA accession Ids and have already downloaded the BAM files in the Galaxy server. Howev… --- ## [Feature count on exon level instead gene level](https://help.galaxyproject.org/t/feature-count-on-exon-level-instead-gene-level/14567)
**Author:** [@Sabsida](https://help.galaxyproject.org/u/Sabsida)\ **Replies:** 3\ **Last updated:** [January 28, 2025, 10:02pm UTC](https://help.galaxyproject.org/t/feature-count-on-exon-level-instead-gene-level/14567 "2025-01-28T22:02:17Z")
Hello dear Galaxy community, I need your help! I have analyzed RNA-seq data by mapping with RNA STAR and then performing featureCounts, followed by DESeq2 and other downstream analyses. Initially, I conducted the analy… --- ## [UCSC Reference Genome and GTF Fatal Error no valid exons in the GTF file](https://help.galaxyproject.org/t/ucsc-reference-genome-and-gtf-fatal-error-no-valid-exons-in-the-gtf-file/14367)
**Author:** [@drcottoncandy](https://help.galaxyproject.org/u/drcottoncandy)\ **Replies:** 3\ **Last updated:** [January 22, 2025, 7:41pm UTC](https://help.galaxyproject.org/t/ucsc-reference-genome-and-gtf-fatal-error-no-valid-exons-in-the-gtf-file/14367 "2025-01-22T19:41:32Z")
Good morning! I am performing RNAstar and feature counts on the species camponotus floridanus. I have followed the tutorial training for RNAseq analysis of d.mel provided by Galaxy, and I had no issues. In this tutorial… --- ## [Genes from my reference genome are not annotated in output files. Trying to get read count per gene/abundant gene list](https://help.galaxyproject.org/t/genes-from-my-reference-genome-are-not-annotated-in-output-files-trying-to-get-read-count-per-gene-abundant-gene-list/13575)
**Author:** [@dpungan](https://help.galaxyproject.org/u/dpungan)\ **Replies:** 1\ **Last updated:** [October 1, 2024, 6:48am UTC](https://help.galaxyproject.org/t/genes-from-my-reference-genome-are-not-annotated-in-output-files-trying-to-get-read-count-per-gene-abundant-gene-list/13575 "2024-10-01T06:48:50Z")
I am trying to analyze RNA-seq fastq files by using Trimmomatric → FastQC → Hisat2 → Cufflinks. I am uploading my reference genome as well as the GTF file but the output files do not include the annotated genes, the gene… --- ## [Intersection between two datasets/lists of genes](https://help.galaxyproject.org/t/intersection-between-two-datasets-lists-of-genes/13190)
**Author:** [@Claire\_Milsted](https://help.galaxyproject.org/u/Claire_Milsted)\ **Replies:** 2\ **Last updated:** [August 24, 2024, 12:53am UTC](https://help.galaxyproject.org/t/intersection-between-two-datasets-lists-of-genes/13190 "2024-08-24T00:53:14Z")
I am trying to create an intersection between two datasets/lists of genes. Specifically, I want to find which values in column 1 of dataset A are also in column 1 of dataset B. If it helps, they are both DESeq2 results t… --- ## [Heatmaps of DEGs presented as z-scores/RNA-seq](https://help.galaxyproject.org/t/heatmaps-of-degs-presented-as-z-scores-rna-seq/13173)
**Author:** [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Replies:** 0\ **Last updated:** [August 8, 2024, 2:05pm UTC](https://help.galaxyproject.org/t/heatmaps-of-degs-presented-as-z-scores-rna-seq/13173 "2024-08-08T14:05:52Z")
Hello, I have used DESeq2 to identify DEGs. What I would like to do next, is to generate a heatmap (via the heatmap2 tool), where I should show those DEGs (cut off: p\<00,5 & -1\1), presented as z-scores. From … --- ## [bedtools intersect intervals](https://help.galaxyproject.org/t/bedtools-intersect-intervals/12746)
**Author:** [@maria22222](https://help.galaxyproject.org/u/maria22222)\ **Replies:** 5\ **Last updated:** [June 21, 2024, 12:57am UTC](https://help.galaxyproject.org/t/bedtools-intersect-intervals/12746 "2024-06-21T00:57:50Z")
Helloo…I run bedtools intersect intervals (-wa option) using as input a bed file containing the genes of an organism and a bed file containing the common peaks i found between 2 MACS2 files. And with the bedtool intersec… --- ## [Title: Scatter plot showing correlation among ChIP-seq and RNA-seq data](https://help.galaxyproject.org/t/title-scatter-plot-showing-correlation-among-chip-seq-and-rna-seq-data/12642)
**Author:** [@Manolis1](https://help.galaxyproject.org/u/Manolis1)\ **Replies:** 2\ **Last updated:** [June 7, 2024, 3:03pm UTC](https://help.galaxyproject.org/t/title-scatter-plot-showing-correlation-among-chip-seq-and-rna-seq-data/12642 "2024-06-07T15:03:57Z")
Hello, I would like to produce a scatter plot among showing the correlation among ChIP-seq data (peaks (TF-binding regions) falling in promoter regions) with RNA-seq data (differentially expressed genes/DEGs from compar… --- ## [error with RNA STAR](https://help.galaxyproject.org/t/error-with-rna-star/12238)
**Author:** [@Maria\_Kamilari](https://help.galaxyproject.org/u/Maria_Kamilari)\ **Replies:** 1\ **Last updated:** [April 17, 2024, 4:39pm UTC](https://help.galaxyproject.org/t/error-with-rna-star/12238 "2024-04-17T16:39:13Z")
Hello all, I can see that the maintenance of the server is over and that jobs should be up and running. However, I continue to get the error " An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/iuc/rg… --- ## [Mstrg convertion into gene symbol. Is this possible?](https://help.galaxyproject.org/t/mstrg-convertion-into-gene-symbol-is-this-possible/11853)
**Author:** [@Georgiapapadim](https://help.galaxyproject.org/u/Georgiapapadim)\ **Replies:** 1\ **Last updated:** [March 5, 2024, 11:36pm UTC](https://help.galaxyproject.org/t/mstrg-convertion-into-gene-symbol-is-this-possible/11853 "2024-03-05T23:36:24Z")
Hello, i am new in bioinformatic analysis and i use galaxy to analyze my rna seq data. I perform rna seq analysis in human milk exosomes. I used STAR for mapping and stringtie for counting my reads. The result came back … --- ## [Problem with Output files with pRESTO via Galaxy](https://help.galaxyproject.org/t/problem-with-output-files-with-presto-via-galaxy/11337)
**Author:** [@silviapc](https://help.galaxyproject.org/u/silviapc)\ **Replies:** 9\ **Last updated:** [January 22, 2024, 9:50pm UTC](https://help.galaxyproject.org/t/problem-with-output-files-with-presto-via-galaxy/11337 "2024-01-22T21:50:49Z")
Hello, I preprocessed sequences with presto via usegalaxy.org using a workflow that I previously ran through the terminal and I got in the output files much less sequences here than with the presto tool via terminal… an… --- ## [Analysis of splice variants.](https://help.galaxyproject.org/t/analysis-of-splice-variants/11221)
**Author:** [@Mukaram\_Bhat](https://help.galaxyproject.org/u/Mukaram_Bhat)\ **Replies:** 4\ **Last updated:** [January 2, 2024, 11:02am UTC](https://help.galaxyproject.org/t/analysis-of-splice-variants/11221 "2024-01-02T11:02:22Z")
What is the recommended workflow in Galaxy for analyzing RNA-seq data, specifically focusing on splice variants? Additionally, how can one convert BAM files to BigWig format using Galaxy? --- ## [problemas herramientas](https://help.galaxyproject.org/t/problemas-herramientas/11173)
**Author:** [@Lauraalvarez](https://help.galaxyproject.org/u/Lauraalvarez)\ **Replies:** 1\ **Last updated:** [November 20, 2023, 5:59pm UTC](https://help.galaxyproject.org/t/problemas-herramientas/11173 "2023-11-20T17:59:35Z")
requiero usar la herramienta “group abundances of UniRef50” pero no la he logrado encontrar en ninguno de las plataformas de los diferentes paises.Es posible que se pueda reemplazar por otra herramienta? O donde la puedo… --- ## [Error with HTseq RNAseq read count](https://help.galaxyproject.org/t/error-with-htseq-rnaseq-read-count/11160)
**Author:** [@Catalina\_Castro](https://help.galaxyproject.org/u/Catalina_Castro)\ **Replies:** 1\ **Last updated:** [November 17, 2023, 1:31am UTC](https://help.galaxyproject.org/t/error-with-htseq-rnaseq-read-count/11160 "2023-11-17T01:31:58Z")
Hi, I am getting error while running HTseq. This is the command and the error: htseq-count -q -f bam -s yes Ac1\_mapped/ac1\_mappedAligned.bam /global/home/users/catalinacastro/star/genome/genomic\_v2.gtf count.txt Er… --- ## [Issue with StringTie](https://help.galaxyproject.org/t/issue-with-stringtie/1996)
**Author:** [@peppe](https://help.galaxyproject.org/u/peppe)\ **Replies:** 4\ **Last updated:** [November 8, 2023, 9:50pm UTC](https://help.galaxyproject.org/t/issue-with-stringtie/1996 "2023-11-08T21:50:58Z")
Hello I was analysing some data using StingTie, initially was working fine, then at some point I start getting an error (it is reported as a tool error). I indeed tried to run again StringTie for a samples that had worke… --- ## [StringTie producing empty column for gene and transcript counts](https://help.galaxyproject.org/t/stringtie-producing-empty-column-for-gene-and-transcript-counts/11054)
**Author:** [@mlawre](https://help.galaxyproject.org/u/mlawre)\ **Replies:** 8\ **Last updated:** [November 6, 2023, 5:45pm UTC](https://help.galaxyproject.org/t/stringtie-producing-empty-column-for-gene-and-transcript-counts/11054 "2023-11-06T17:45:49Z")
Hi I’m new to Galaxy and trying to to perform DEG from RNA-seq for 3 conditions with 3 reps (9 total samples) but have fallen off track by getting empty columns for gene counts at the Stringtie step. The workflow has bee… --- ## [fgsea of gene sets in .gmt does not provide any output](https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099)
**Author:** [@Sebastian](https://help.galaxyproject.org/u/Sebastian)\ **Replies:** 1\ **Last updated:** [November 6, 2023, 1:22pm UTC](https://help.galaxyproject.org/t/fgsea-of-gene-sets-in-gmt-does-not-provide-any-output/11099 "2023-11-06T13:22:18Z")
Hello everyone, I would like to do a gene set enrichment analysis using the fgsea tool. Everything works fine if I use the common Hallmark gene set from WEHI Bioinformatics - mouse and human versions of the MSigDB in R… --- ## [Smart-seq2 data analysis](https://help.galaxyproject.org/t/smart-seq2-data-analysis/10420)
**Author:** [@btilouche](https://help.galaxyproject.org/u/btilouche)\ **Replies:** 2\ **Last updated:** [November 2, 2023, 2:53pm UTC](https://help.galaxyproject.org/t/smart-seq2-data-analysis/10420 "2023-11-02T14:53:34Z")
Hi, I have downloaded FASTQ files from a single cell experiment that used SMART-seq2. As you know, this pipeline generates 2 read files per single cell. I am able to allign the reads using HISAT2, however, I am not sure… --- ## [Deseq2 analysis output too many DEGs](https://help.galaxyproject.org/t/deseq2-analysis-output-too-many-degs/11043)
**Author:** [@brebelo](https://help.galaxyproject.org/u/brebelo)\ **Replies:** 1\ **Last updated:** [October 26, 2023, 4:27pm UTC](https://help.galaxyproject.org/t/deseq2-analysis-output-too-many-degs/11043 "2023-10-26T16:27:26Z")
Hello everyone. I have two samples, WT and Mutant. I performed Featurecounts, obtained the count file, remove reads bellow 20 counts and perform the deseq2 analysis. However, even filtering pvalue\<0.001 and a fold chang… --- ## [RNA-Seq analysis in Galaxy](https://help.galaxyproject.org/t/rna-seq-analysis-in-galaxy/10945)
**Author:** [@Ahmad\_B](https://help.galaxyproject.org/u/Ahmad_B)\ **Replies:** 11\ **Last updated:** [October 25, 2023, 12:17am UTC](https://help.galaxyproject.org/t/rna-seq-analysis-in-galaxy/10945 "2023-10-25T00:17:01Z")
Hello I have a problem to use the featurecount part in Galaxy database. My RNA-Seq data about arabidopsis thaliana. I use the external genome file from my computer I downloaded from ensemble genome browser. Then I uploa… --- ## [Problem in DESe2 with multiple factors](https://help.galaxyproject.org/t/problem-in-dese2-with-multiple-factors/11035)
**Author:** [@des\_b](https://help.galaxyproject.org/u/des_b)\ **Replies:** 3\ **Last updated:** [October 24, 2023, 11:06am UTC](https://help.galaxyproject.org/t/problem-in-dese2-with-multiple-factors/11035 "2023-10-24T11:06:43Z")
Hi all, I am currently analysing my data from an RNA-seq experiment. I have brain tissue for mice, and I aim to find differentially expressed genes. I am using the DESeq2 tool, and I follow the instructions of the tutor… --- ## [Basic Question - FPKM Count - What do I use as the reference gene model?](https://help.galaxyproject.org/t/basic-question-fpkm-count-what-do-i-use-as-the-reference-gene-model/10895)
**Author:** [@Quantum\_Bean](https://help.galaxyproject.org/u/Quantum_Bean)\ **Replies:** 1\ **Last updated:** [October 19, 2023, 11:48pm UTC](https://help.galaxyproject.org/t/basic-question-fpkm-count-what-do-i-use-as-the-reference-gene-model/10895 "2023-10-19T23:48:12Z")
Hey all, I am new to Galaxy and Seq-analysis in general so have a basic questions… For FPKM Count you need 2 inputs 1) the bam file from RNA-seq which I have, and 2) a reference gene model in the form of a BED12 data se… --- ## [DEseq2 and why it requires replicates](https://help.galaxyproject.org/t/deseq2-and-why-it-requires-replicates/10987)
**Author:** [@Alok\_Dubey](https://help.galaxyproject.org/u/Alok_Dubey)\ **Replies:** 1\ **Last updated:** [October 17, 2023, 4:30pm UTC](https://help.galaxyproject.org/t/deseq2-and-why-it-requires-replicates/10987 "2023-10-17T16:30:53Z")
Hello every one im working on miRNA data set i have performed fastqc to miRNA qunatification using fastqc and mirdeep2 quantifier respectively. After qunatification i had used cut on table for tabular data then i used DE… --- ## [Help with interpreting GO enrichment resutls using goseq](https://help.galaxyproject.org/t/help-with-interpreting-go-enrichment-resutls-using-goseq/10938)
**Author:** [@ding66](https://help.galaxyproject.org/u/ding66)\ **Replies:** 6\ **Last updated:** [October 12, 2023, 9:28pm UTC](https://help.galaxyproject.org/t/help-with-interpreting-go-enrichment-resutls-using-goseq/10938 "2023-10-12T21:28:03Z")
Hi there! I’m new to RNA-Seq results analysis. By following the tutorial of " Reference-based RNA-Seq data analysis" (Reference-based RNA-Seq data analysis), I have so far completed mapping, annotation, differential expr… --- ## [Question regarding goseq in RNA-SEQ tutorial](https://help.galaxyproject.org/t/question-regarding-goseq-in-rna-seq-tutorial/10269)
**Author:** [@mfaleevs](https://help.galaxyproject.org/u/mfaleevs)\ **Replies:** 2\ **Last updated:** [September 28, 2023, 8:19am UTC](https://help.galaxyproject.org/t/question-regarding-goseq-in-rna-seq-tutorial/10269 "2023-09-28T08:19:40Z")
I am working through the Reference based RNA-SEQ data analysis tutorial and am at the stage where the differentially expressed genes are being run through goseq. However, I see that in the previous step (compute), we onl… --- ## ["error in importRdata" using isoformswitchanalyzR](https://help.galaxyproject.org/t/error-in-importrdata-using-isoformswitchanalyzr/10399)
**Author:** [@Margaret\_M](https://help.galaxyproject.org/u/Margaret_M)\ **Replies:** 14\ **Last updated:** [September 12, 2023, 5:22pm UTC](https://help.galaxyproject.org/t/error-in-importrdata-using-isoformswitchanalyzr/10399 "2023-09-12T17:22:27Z")
Hello, I’m trying to run isoformswitchanalyzR, my history is here: Galaxy | Europe I seem to be having a problem with the reference transcriptome not matching with my quantified data. My error message: “Step 1 of 7: … --- ## [DESeq2 with pair end file (Stringtie)](https://help.galaxyproject.org/t/deseq2-with-pair-end-file-stringtie/10734)
**Author:** [@Seongmoon\_Jo](https://help.galaxyproject.org/u/Seongmoon_Jo)\ **Replies:** 1\ **Last updated:** [September 5, 2023, 8:50pm UTC](https://help.galaxyproject.org/t/deseq2-with-pair-end-file-stringtie/10734 "2023-09-05T20:50:30Z")
Hello, I have a question about DESeq2 with pair end file. I generated StringTie on collection from pair end, RNA-seq raw data. However, I can’t put on each file for factor level of DESeq2. How can I solve this? [Next page](https://help.galaxyproject.org/tag/rna-seq/400.md?match_all_tags=true&page=1&tags%5B%5D=rna-seq)