question about the equation of counts in STAR ReadsPerGene.out.tab

Question

[boymin2020]

Hi,

Recently I have been evaluating gene expression levels using STAR software. Regarding the counts in the ReadsPerGene.out.tab table, I am confused about the equation of N_unmapped (12935190), N_multimapping(6553338), N_noFeature(4320607), N_ambiguous(1013776) and the sum of readspergene (12473764).

The additional file is the Log.final.out as shown below. Could you help to correlate all of the reads information? Better in equations.

                                Started job on |       Dec 03 17:38:54
                             Started mapping on |       Dec 03 19:50:36
                                    Finished on |       Dec 03 21:04:20
       Mapping speed, Million of reads per hour |       20.07

                          Number of input reads |       24660208
                      Average input read length |       200
                                    UNIQUE READS:
                   Uniquely mapped reads number |       17808147
                        Uniquely mapped reads % |       72.21%
                          Average mapped length |       110.21
                       Number of splices: Total |       4853399
            Number of splices: Annotated (sjdb) |       4841181
                       Number of splices: GT/AG |       4792927
                       Number of splices: GC/AG |       40247
                       Number of splices: AT/AC |       7008
               Number of splices: Non-canonical |       13217
                      Mismatch rate per base, % |       10.54%
                         Deletion rate per base |       0.04%
                        Deletion average length |       2.35
                        Insertion rate per base |       0.03%
                       Insertion average length |       2.28
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |       6553338
             % of reads mapped to multiple loci |       26.57%
        Number of reads mapped to too many loci |       291711
             % of reads mapped to too many loci |       1.18%
                                  UNMAPPED READS:
  Number of reads unmapped: too many mismatches |       4348
       % of reads unmapped: too many mismatches |       0.02%
            Number of reads unmapped: too short |       0
                 % of reads unmapped: too short |       0.00%
                Number of reads unmapped: other |       2664
                     % of reads unmapped: other |       0.01%
                                  CHIMERIC READS:
                       Number of chimeric reads |       0
                            % of chimeric reads |       0.00%

Answer 1

[h.mon]

See answer A: Difference between read counts STAR vs featureCounts .