I am currently trying to find number of reads (sequenced from DNAseq) that are mapped to human genes. So I tried three different methods to validate whether I am getting the same read count. 1) samtools 2) featurecount 3) htseq-count
For example, considering this gene "WASH7p". As per the human GTF downloaded from UCSC for hg19, I have following exons in them.
Method1: using samtools command
Total read count as per samtools: 6
htseq-count -f bam -s no -i gene_id Sample_001_TGACCA_L001.bam Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf > Sample_001_Read_count_based_on_gene.txt 2>Sample_001_htseq_count.log &
Why htseq-count is giving "0"? Am I missing some parameters?