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  • 2nd Pass Alignment with STAR for RNA-sequencing

    Hello everyone,

    Firstly, thanks for reading this post. I'm performing 2nd pass alignment with STAR and I was wondering how to merge SJ.out.tab files. I'll be performing the first phase alignment on ~21 files and will need to merge 21 SJ.out.tab files. I couldn't find an explanation in the manual on how to merge these files prior to creating a new genome index for the second pass.

    I appreciate your time,
    cbaudo

  • #2
    I'm also having trouble with this concept.
    Last edited by mmackattack; 03-03-2015, 08:43 AM.

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    • #3
      Hopefully your directory structure is setup in such a way, that you can do something along the lines of:

      cat /path/to/my/project/results/alignments/mySample*/SJ.out.tab >/path/to/desired/output/directory/all.SJ.out.tab

      Where the asterix could be e.g.: 01,02,...,21

      Cheers,
      Leon

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      • #4
        Many thanks, Leon.

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