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• Mm9 Reference Gtf File For Cuffcompare
  I wonder if some has mouse genome GTF file compatible with Tophat/ Cuffcompare. The contig names ...
• RNA-seq analysis in Galaxy
  I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia...
• How to upload Mouse reference genome mm10, in Fasta format to My Galaxy History
  I tried to use an imported "tuxedo protocol" RNA-seq pipeline from public workflows. I found mous...
• gtf file for chicken
  Dear all, Where i can download gtf file of chicken (Gallus Gallus) for reference annotation step ...
• A Simple Operation Didn'T Work Out
  Hi All, I got a bit disappointed when I failed in the following operation which seems to be simp...
• Gene annotation for cuffdiff/cufflink
  I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, an...
• RNA Star problems
  I am pretty new in Galaxy. I have been following some tutorials in order to perform some DEG with...
• featureCounts 1.6.0.3 using reference annotation GTF from the history
  I used featureCounts about two weeks ago on one dataset and had no issues. Today I tried running ...
• Cufflinks Error With Illumina Igenome .Gtf For Annnotation
  Hi all, I am attempting to use tophat>cufflinks>cuffmerge>cuffdiff to compare transcri...
• iGenomes UCSC hg38 annotation gtf file
  Dear community, I have been analysing rna-seq data using Tuxedo on galaxy. I download the iGeno...
• Cuffcompare Input
  dear forum, I have two samples, treated and untreated. When I run cuffcompare (to created the gtf...
• Query in uploading data in stringtie
  When I am using stringtie in galaxy, the one option is **Reference annotation to use for guiding ...
• Non-Coding Rna Annotation
  Hi all, I am analyzing my small RNA sequencing data on mouse tissue. Does anyone know where to do...
• gtf file error
  Dear all, My reference genome is Duck, not index in Galaxy reference genome. So i downloaded fast...
• Annotation File For Cufflinks
  Hi jen and galaxy users, when I try to use cufflinks in GALAXY and select "use reference annotati...
• Is this correct way ??
  Dear Sir, while doing RNA-Seq analysis, after mapping, i have downloaded mouse reference gene se...
• Salmon human GTF or tabular annotation reference input dataset
  Hello I would like to use salmon to do RNA seq analysis. I run it successfully with ensembl refe...
• converting .gff file to .gtf
  I am using galaxy rnaseq workflow. I have my annotation file in .gff format, however it needs the...
• Question About Formattung Mouse (Mm9) Gtf
  I have read in the mailing list that you have a workflow which can modify the human GTF file so ...
• Should I Use Igenomes Verson Of A Reference Gtf For Tophat?
  Dear All, I am analysing RNA-seq datasets for differential splicing events between cell types. T...