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Mapping to the TranscriptID

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

rna-seq alignment
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updated by Ram Ram • written by essepf • essepf

1 answer

Try something that handles splicing, like STAR or tophat2.

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written by Devon Ryan Devon Ryan

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