Mapping to the TranscriptID

Question

[essepf]

Hello

I have 100 sequences, each sequence with 100 bp.

I map to the genome reference (used bowtie2), but some of them were not mapped (not genomic). The solution is map this sequences to the transcript.

At this time suggest something like Trinity or Cufflinks.

What you suggest me? more quickly and effectively?

Thank you very much

SFC

Answer 1

[Devon Ryan]

Try something that handles splicing, like STAR or tophat2.