multiBamCov or htseq-count to count read per feature ?

[NicoBxl]

Hi,

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 ?

Thanks,

N.

[dawe]

AFAIK htseq-count supports several ways to perform the intersection, hence you may want to post the actual command lines with all parameters used. multiBamCov supports flag filtering.
What do you mean by strictness here?