Question: featurecount command to extract read count from bam files
1
gravatar for krushnach80
5 months ago by
krushnach80160
krushnach80160 wrote:

I m using this featurecount command to extract read count from my bam files , is it the correct one im using or there is some issue with my command .

featureCounts -T 40 -p -A  -s -f -O -t exon -g gene_id -a /home/punit/ERCCgencode.v21.annotation.gtf -o /home/punit/FCOUNT/newhl60.txt ~/bamfiles/WT1.bam ~/bamfiles/WT2.bam ~/bamfiles/AT1.bam ~/bamfiles/AT2.bam ~/bamfiles/VD1.bam ~/bamfiles/VD2.bam
rna-seq • 250 views
ADD COMMENTlink modified 5 months ago by Devon Ryan71k • written 5 months ago by krushnach80160
4
gravatar for Devon Ryan
5 months ago by
Devon Ryan71k
Freiburg, Germany
Devon Ryan71k wrote:
  • -A takes a file with chromosome name aliases, which you're not providing and likely don't need.
  • -s takes a number indicating what sort of strand specificity you want. You likely want -s 2.
  • If you want to use these in edgeR/DESeq2/etc., don't use -O.
    • You probably don't want -f.

In general, run commands first and spot-check the results to see if anything went wrong. Also, start using new commands/tools by using the defaults.

ADD COMMENTlink written 5 months ago by Devon Ryan71k

yes Im using the output for deseq2

ADD REPLYlink written 5 months ago by krushnach80160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1461 users visited in the last hour