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 



 * `-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.