I am using publicly available RNA-seq data from GEO. I am using Tophat2>featureCounts>DESeq2 pipeline with hg19 genome build. The count table given in geo has 38k reads while the one I generated with featurecounts gives 66k. I do not have any idea what can cause this problem. Or how to fix? Is there someone had or having this problem?
Thank you for helps.