Question: featurecount command to extract read count from bam files
1
gravatar for krushnach80
13 months ago by
krushnach80300
krushnach80300 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 • 838 views
ADD COMMENTlink modified 13 months ago by Devon Ryan81k • written 13 months ago by krushnach80300
4
gravatar for Devon Ryan
13 months ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k 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 13 months ago by Devon Ryan81k

yes Im using the output for deseq2

ADD REPLYlink written 13 months ago by krushnach80300
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