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03-03-2015, 08:31 AM
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#1 |
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Member
Location: Missouri Join Date: Jan 2013
Posts: 21
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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 |
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03-03-2015, 08:35 AM
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#2 |
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Junior Member
Location: st louis Join Date: Mar 2015
Posts: 1
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I'm also having trouble with this concept.
Last edited by mmackattack; 03-03-2015 at 08:43 AM. |
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03-03-2015, 10:44 PM
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#3 |
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Member
Location: Denmark Join Date: Sep 2014
Posts: 69
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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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03-04-2015, 04:59 AM
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#4 |
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Member
Location: Missouri Join Date: Jan 2013
Posts: 21
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Many thanks, Leon.
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| Tags |
| alignment, rna-sequencing, sj.out.tab, star |
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