Recommended doc for interpreting STAR alignment stats

Question

[emblake]

I ran STAR (v2.5.2b) to map 30 100bp PE reads, and I'm curious if anyone can recommend any documentation to interpret the alignment stats found in the Log.final.out file? Is there a guide that mentions ranges for poor or good quality stats? The STAR manual does not go into detail for each parameter.

Sample file output:

                             Started job on |       Oct 19 15:13:30
                         Started mapping on |       Oct 19 15:15:14
                                Finished on |       Oct 19 15:20:37
   Mapping speed, Million of reads per hour |       309.93

                      Number of input reads |       27807734
                  Average input read length |       194
                                UNIQUE READS:
               Uniquely mapped reads number |       20450138
                    Uniquely mapped reads % |       73.54%
                      Average mapped length |       192.66
                   Number of splices: Total |       9387626
        Number of splices: Annotated (sjdb) |       9106647
                   Number of splices: GT/AG |       9247743
                   Number of splices: GC/AG |       76354
                   Number of splices: AT/AC |       7323
           Number of splices: Non-canonical |       56206
                  Mismatch rate per base, % |       0.18%
                     Deletion rate per base |       0.01%
                    Deletion average length |       1.47
                    Insertion rate per base |       0.01%
                   Insertion average length |       1.36
                         MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |       5996936
         % of reads mapped to multiple loci |       21.57%
    Number of reads mapped to too many loci |       61402
         % of reads mapped to too many loci |       0.22%
                              UNMAPPED READS:
   % of reads unmapped: too many mismatches |       0.00%
             % of reads unmapped: too short |       4.63%
                 % of reads unmapped: other |       0.04%
                              CHIMERIC READS:
                   Number of chimeric reads |       0
                        % of chimeric reads |       0.00%

Answer 1

[Jeffin Rockey]

STAR author has given detailed explanations on the stat numbers in various posts at https://groups.google.com/forum/m/#!forum/rna-star

Hope it helps.