Should RNA-seq libraries be aligned in parallel or consecutively?

Mark74Mark74 LeicesterMember

Hi,
I'm mapping several RNA-seq libraries to a genome with the aim of detecting nucleotide variation. I'm following the protocol "Calling variants in RNAseq".
Is it possible to do them in parallel - mapping all libraries to the genome and detecting splice junctions etc. simultaneously - or does the whole protocol need to be followed separately for each library?
Thank you,
Mark

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by Sheila

Issue Number
241
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vdauwera

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Hi Mark,

    The mapping needs to be done independently for each library, because of how the tools assign read group information to the data. In the case of RNAseq you can have STAR aligner add read group information to the mapped output, which is very convenient. If you're using a computing cluster you can run mapping in true parallel fashion on the libraries, ie launch all the separate jobs in parallel on different nodes, which will be faster (in "wall clock time") than running them one after the other on a single machine.

    I've heard some people apply the same splice junctions to all libraries, but I can't give you details -- you'd have to ask on the STAR mailing list how that would work.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Hi Mark,

    The mapping needs to be done independently for each library, because of how the tools assign read group information to the data. In the case of RNAseq you can have STAR aligner add read group information to the mapped output, which is very convenient. If you're using a computing cluster you can run mapping in true parallel fashion on the libraries, ie launch all the separate jobs in parallel on different nodes, which will be faster (in "wall clock time") than running them one after the other on a single machine.

    I've heard some people apply the same splice junctions to all libraries, but I can't give you details -- you'd have to ask on the STAR mailing list how that would work.

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