I'm wondering what is the best method to extract the number of reads for each feature in a gtf (or gff, bed,...) file. I tried htseq-count and multiBamCov but they gave me different results.it seems that multiBam count all the reads (complete and partial aligned) associated with each exon. It means there are many reads are count twice or more time.
After doing DE analysis (DESeq) on both read count matrix (one from htseq, one from multiBamCov), the results are quite surprising.
pval adjusted < 0.05 multiBamCov : 123 gene differentially expressed htseq : 880 gene
Intersection : 118 gene
So which one to use ? is it possible to change multiBamCov to be more strict ? maybe is it possible to use other tools from bedtools ?