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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
yueli
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Location: china

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Default suitable aligner for human RNA-seq

Hello,

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!

Sincerely,

Yue
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Old 05-02-2018, 05:01 AM   #2
colindaven
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STAR or Hisat2, and NOT Tophat2
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aligner, genome, human, illumina, rna-seq

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