What is the best aligner for stranded RNASeq
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14 months ago
tarek.mohamed ▴ 370

Hello,

What is the best aligner for stranded RNASeq?

Thanks

aligner stranded RNAseq • 650 views
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14 months ago

If you only need to quantify expression at the transcript/gene level, use Salmon or Kallisto. If you need to align reads to the transcriptome or genome go with STAR.

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14 months ago
jkim ▴ 170

Not sure about the best aligner, but there are some aligners that widely used, such as STAR or HISAT2. I saw some article comparing aligners using simulating data. If I remember it correctly, GSNAP and STAR did pretty good jobs.

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