Hello,
I am new to bioinformatics and the Galaxy user interface. I am currently trying to analyze RNAseq data using the online Galaxy program. We typically have a company run all of the mapping for us and use the counts files from them to use DEseq2. We had an issue with our latest data set and I want to try and create the counts tables myself from the BAM files they have sent. I have an old data set with both BAM and counts files that I am using to try and generate the exact counts tables they gave. The company has sent the exact code used to generate our counts tables however, they use the programming language and I am using the web-based Galaxy. The user interface is easy to understand and I have been able to replicate most of the parameters used by the company except for the thread number (-T). The company uses this code:
featureCounts -f -O -s 0 -p -T 8 -F GTF -t exon -a <GTF> -o <output.counts.txt> <Input.bam>
From the online help I could find, this means they use a thread number of 8. On the galaxy website however, I cannot find a way to change this which has brought me here..
- What exactly is the thread number? I have seen it classified as the processing power? Is this correct?
- Is there a way to change this on the featureCounts tool on the Galaxy website?
- Does this number impact the count values generated? I seem to be able to recapitulate many of the values but some are slightly different and am wondering if this is due to the thread specification.
Thank you for any help/advice you can provide!
