This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Strand-Specific Rna-Seq Alignment

Hi,

Is there a list of strand-specific RNA-seq aligners ? For now I use tophat 2 with strand-specific parameter but I want to try other tools.

Thanks,

N.

rna-seq strand alignment
• 6,570 views • link
updated by Rohit Rohit • written by Nicolas Rosewick Nicolas Rosewick

Have you tried to search for related questions at biostars? Questions are conveniently categorized by tagging them. This way, the tag RNA-seq includes 162 threads, many of them discussing alignment.

• 0 views • link
written by Irsan Irsan

I made a serach with "Strand-specific RNA-seq alignment" but nothing helpfull came out.

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

1 answer

Dissect is another tool for alignment.

Bowtie works fine but for RNA-seq you might get many unaligned reads as it does not support alternative splicing, go for the --local option with less stringency.

• 0 views • link
written by Rohit Rohit

I you use bowtie, better use tophat (which use bowtie) and is splice aware.

• 63 views • link
written by Nicolas Rosewick Nicolas Rosewick

Log in to answer this question.

More posts like this