I have aligned my RNAseq data to the reference genome and extracted raw count using
featureCounts tool. I used two different GTF file from NCBI, one having only Refseq id as gene_id and other having gene symbol as gene_id.
Refseq as gene_id
chr11 mm10_refGene exon 100883834 100885169 0.000000 + . gene_id "NM_001164062"; transcript_id "NM_001164062";
Gene symbol as gene_id
chr11 stdin exon 100883834 100885169 . + . gene_id "Stat5a"; transcript_id "NM_001164062"; exon_number "18"; exon_id "NM_001164062.18"; gene_name "Stat5a";
Surprisingly when I looked into the raw count for above feature that I have highlighted is showing different count from
featuteCounts output for these two different GTF file It would be really great if someone could help me understanding these different results or If I am missing something here.
gene_id Count NM_001164062 0 NM_011488 11 Stat5a 14046
Here is the code that I used to extract the count
featureCounts --verbose -p -B -T 20 -a mm10_refseq.gtf -o Emp Emp_R1.sorted.bam
and IGV browser snapshot of the bam coverage at the highlighted features.