Question: Strand-Specific Rna-Seq Alignment
1
gravatar for Nicolas Rosewick
6.5 years ago by
Belgium, Brussels
Nicolas Rosewick7.9k wrote:

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.

alignment rna-seq strand • 4.1k views
ADD COMMENTlink modified 6.4 years ago by Rohit1.4k • written 6.5 years ago by Nicolas Rosewick7.9k

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.

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by Irsan6.9k

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

ADD REPLYlink written 6.5 years ago by Nicolas Rosewick7.9k
1

Then Is Tophat The Only Mapper To Consider For Rna-Seq Data?

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by Irsan6.9k

ok great! thanks

ADD REPLYlink written 6.5 years ago by Nicolas Rosewick7.9k

This post: Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads also has many relevant answers

ADD REPLYlink written 6.3 years ago by Malachi Griffith17k
0
gravatar for Rohit
6.4 years ago by
Rohit1.4k
California
Rohit1.4k wrote:

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.

ADD COMMENTlink written 6.4 years ago by Rohit1.4k
1

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

ADD REPLYlink written 6.3 years ago by Nicolas Rosewick7.9k
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