Merge STAR files together
Entering edit mode
4 weeks ago
minifoog • 0

Say I have multiple files like this:

An example of what the .out file looks like:

                             Started job on |   Apr 23 23:17:02
                         Started mapping on |   Apr 23 23:17:04
                                Finished on |   Apr 23 23:26:52
   Mapping speed, Million of reads per hour |   115.68

                      Number of input reads |   18894432
                  Average input read length |   298
                                UNIQUE READS:
               Uniquely mapped reads number |   17704240
                    Uniquely mapped reads % |   93.70%
                      Average mapped length |   297.39
                   Number of splices: Total |   3119841
        Number of splices: Annotated (sjdb) |   2663436
                   Number of splices: GT/AG |   3080422
                   Number of splices: GC/AG |   14219
                   Number of splices: AT/AC |   248
           Number of splices: Non-canonical |   24952
                  Mismatch rate per base, % |   0.49%
                     Deletion rate per base |   0.02%
                    Deletion average length |   2.70
                    Insertion rate per base |   0.02%
                   Insertion average length |   2.30
                         MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |   806405
         % of reads mapped to multiple loci |   4.27%
    Number of reads mapped to too many loci |   1146
         % of reads mapped to too many loci |   0.01%

I want to make a .csv file where I only take: Number of input reads, Uniquely mapped reads number, and Uniquely mapped reads %. Is there a tool that can do this? Any help would be appreciated.

alignment STAR compile • 240 views
Entering edit mode
4 weeks ago

MultiQC understands STAR logs (see extension notes here). After running MultiQC, there's a json object which you can parse of the accumulated reports if that's more in line with what you have in mind.

Entering edit mode

Thanks for the comment!

Entering edit mode
4 weeks ago
Malcolm.Cook ★ 1.2k

STAR comes with a script that merges files from multiple runs into one table


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