featureCount and bam

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Morris ▴ 10

@morris-13226

Last seen 17 months ago

Italy

Hi,

I installed Rsubread and now I want to extract raw counts from RNAseq bam files.
Could you please give me the command line to use in order to analyse one or more bam files?

thank you

featurecounts • 2.9k views

ADD COMMENT • link 7.6 years ago Morris ▴ 10

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Did you find the manual? It's all in there.

ADD REPLY • link 7.6 years ago b.nota ▴ 370

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Hi b.note, I found the manual thanks.
Let me summarize just to see if I m on the right way...
I have two bam files and I want to perform a differential expression analysis. The first thing to do is to use featureCounts to align and count the reads for all the genes contained in each file.
Is this correct?

The first command line from futureCounts is this:

featureCounts -T 5 -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_SE.sam

but I don't know each word what it is, for example 5 are threads, but what is a treads ?
basically what is required to make this command line working ?

thank you

-P

ADD REPLY • link 7.6 years ago Morris ▴ 10

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Remember that you are working in R with Rsubread, the command line you use now in for bash/linux.

What you need is your bam files, and an annotation file in gtf format. The threads are the number of processors in your computer system, if you have more than one you can define them here. If you use a model organism (mouse, human), you could probably use the inbuilt annotation.

See here for full exaplanation of the function in R:

ADD REPLY • link 7.6 years ago b.nota ▴ 370

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