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• using SAF gene annotation file in featurecounts
  Hello! I'm new to Galaxy and was wondering if I could get some help with using the featurecounts...
• Content of the built-in hg38 genome annotation available in Featurecounts
  Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy ...
• Featurecounts on Galaxy main
  I have a general question/issue I wonder if anyone knows a solution to. Firstly, as I said in a p...
• featureCounts jobs will not submit unless input BAM(s) have the "database" metadata assigned
  Hello, I am trying to run featureCounts on my BAM file using a built-in genome from Galaxy. I wro...
• Locally cached annotation not available for featureCounts
  Hi all, For my RNAseq analysis, I am using the featureCounts tool to measure gene expression fr...
• Incoperating Annotations (from a GFF file) to a custom built genome
  Hi, I created a custom build using the rubber genome available at NCBI. I would like to incorpor...
• Featurecounts built-in annotation hg38, hg19, mm10, mm9
  "Parameter genome requires a value, but has no legal values defined" stop me from execution. whic...
• featureCounts doesn't recognize Rat annotation file in history, what am I doing wrong?
  Dear Experts, I use Htsat2 output file for running feature-counts, but when I set up the run Gala...
• Papio Anubis 2.0 genome annotation
  Hello, I was wondering if there was a possibility of adding the papAnu_2.0 annotation as a built...
• 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 ...
• featureCounts gives extreme low counts on highly expressed genes
  I mapped paired-end sequencing with RNA-STAR and got the BAM file. I then use featureCounts to co...
• Ngs With Arabidopsis Thaliana Built-In-Index
  Hi all, I've been having trouble running my Arabidopsis thaliana NGS pipeline in galaxy. Specifi...
• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...
• FeatureCounts from GUI galaxy
  I ran featurecounts from Galaxy GUI – it didn’t recognized genomic annotation UCSC from history. ...
• Can't use cached bed file
  Hey, I wanted to have built-in BED files specific to the genome references that I added to my lo...
• Duplicate Row Removal in Merged FeatureCounts
  Hello,   I am trying to transfer merged featurecount data into an R-studio package called RNASe...
• Unable to select GTF file from history in featureCounts (Galaxy version 1.6.0.3)
  Hello, I have recently begun mapping Drosophila RNA-Seq data with STAR (in Galaxy), and I am now...