Question: Recommended doc for interpreting STAR alignment stats
0
gravatar for emblake
3.0 years ago by
emblake50
United States
emblake50 wrote:

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%
rna-seq star alignment • 1.7k views
ADD COMMENTlink modified 3.0 years ago by Jeffin Rockey1.1k • written 3.0 years ago by emblake50
1
gravatar for Jeffin Rockey
3.0 years ago by
Jeffin Rockey1.1k
Karimannoor
Jeffin Rockey1.1k wrote:

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.

ADD COMMENTlink written 3.0 years ago by Jeffin Rockey1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1657 users visited in the last hour