running featureCounts on multiple bam files

Question

[Mamta]

Hi,

Could you please have a look on below command and can suggest if it is the correct command to run on multiple sorted bam file to generate the count matrix for gene expression analysis. I also want to get TPM count after this raw count but not sure if there is any package available to convert raw count to TPM count.

featureCounts -t exon -g gene_id -a GCF_019359855.2_Ky_2.0_genomic.gtf -T 10  -o counts.txt PR10C01.sorted.bam PR10C02.sorted.bam PR10C03.sorted.bam PR10C04.sorted.bam 

Many thanks,

Answer 1

[GenoMax]

Be sure to add -p --countReadPairs options to this command if you have paired-end reads. Otherwise that command looks good.

Not sure why you need TPM but read through this thread: Get TPM from RNA counts and gene length?

If you still want TPM's then the answer here should help --> Raw counts to TPM in R

[Mamta]

thank yo so much @genomax. all sorted.