I'm analysing RNA-Seq data to finally calculate RPKM value. First I did denovo assembly of reads using Trinity assembler. Then using Trinity output as reference for bowtie2, against same reads (used for denovo assembly) for mapping. But when I ran htseq, it gives zero read counts for some trinity contigs, since I used same reads for assembly and mapping, I shouldn't get zero read count.
here is a workflow:
Trinity -> bowtie2 -> htseq -> RPKM
Ideally I should not get zero read count for any of the trinity contigs, since all contigs were created from same reads. I don't understand where it went wrong.
Any help would be appreciated Thanks