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best suitable aligner for RNA-seq mapping yueli Illumina/Solexa 2 04-19-2018 08:16 AM

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Old 04-19-2018, 07:42 AM   #1
Location: china

Join Date: May 2013
Posts: 71
Default suitable aligner for human RNA-seq


Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

The first step is making alignment of the reads to the human genome. These are many aligner, such as: Bowtie, GASSST, PASS, SOAP, BOAT. Each aligners has different performs in different kinds of data.

Which is the best suitable aligner for RNA-seq data?

Thank you in advance for great help!


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yueli is offline   Reply With Quote
Old 05-02-2018, 05:01 AM   #2
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Location: Germany

Join Date: Oct 2008
Posts: 415

STAR or Hisat2, and NOT Tophat2
colindaven is offline   Reply With Quote

aligner, genome, human, illumina, rna-seq

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