MultiQC for STAR alignment incorrect

[Huiting120]

Description of the bug

STAR produces 2 alignment report files: pairedLog.final.out and singleLog.final.out. When MultiQC is generating the report, instead of combining them, seems like it randomly grabbed one. This bug needs to be fixed.

Command used and terminal output

No response

Relevant files

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System information

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[Huiting120]

Output from the pairedLog.final.out:

                          Number of input reads |       35924429
                      Average input read length |       299
                                    UNIQUE READS:
                   Uniquely mapped reads number |       30437677
                        Uniquely mapped reads % |       84.73%
                          Average mapped length |       293.64
                       Number of splices: Total |       23823286
            Number of splices: Annotated (sjdb) |       0
                       Number of splices: GT/AG |       23351051
                       Number of splices: GC/AG |       252193
                       Number of splices: AT/AC |       13303
               Number of splices: Non-canonical |       206739
                      Mismatch rate per base, % |       1.24%
                         Deletion rate per base |       0.13%
                        Deletion average length |       3.71
                        Insertion rate per base |       0.09%
                       Insertion average length |       3.38
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |       1517679
             % of reads mapped to multiple loci |       4.22%
        Number of reads mapped to too many loci |       3189
             % of reads mapped to too many loci |       0.01%
                                  UNMAPPED READS:
  Number of reads unmapped: too many mismatches |       0
       % of reads unmapped: too many mismatches |       0.00%
            Number of reads unmapped: too short |       3962934
                 % of reads unmapped: too short |       11.03%
                Number of reads unmapped: other |       2950
                     % of reads unmapped: other |       0.01%
                                  CHIMERIC READS:
                       Number of chimeric reads |       0
                            % of chimeric reads |       0.00%

Output from singleLog.final.out

                          Number of input reads |       918562
                      Average input read length |       147
                                    UNIQUE READS:
                   Uniquely mapped reads number |       742328
                        Uniquely mapped reads % |       80.81%
                          Average mapped length |       145.50
                       Number of splices: Total |       227386
            Number of splices: Annotated (sjdb) |       0
                       Number of splices: GT/AG |       221809
                       Number of splices: GC/AG |       2080
                       Number of splices: AT/AC |       101
               Number of splices: Non-canonical |       3396
                      Mismatch rate per base, % |       1.77%
                         Deletion rate per base |       0.15%
                        Deletion average length |       3.57
                        Insertion rate per base |       0.10%
                       Insertion average length |       3.17
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |       44739
             % of reads mapped to multiple loci |       4.87%
        Number of reads mapped to too many loci |       160
             % of reads mapped to too many loci |       0.02%
                                  UNMAPPED READS:
  Number of reads unmapped: too many mismatches |       0
       % of reads unmapped: too many mismatches |       0.00%
            Number of reads unmapped: too short |       131300
                 % of reads unmapped: too short |       14.29%
                Number of reads unmapped: other |       35
                     % of reads unmapped: other |       0.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |       0
                            % of chimeric reads |       0.00%

Numbers from the MultiQC report:

Uniquely mapped: 742328
Mapped to multiple loci: 44739
Mapped to too many loci: 160
Unmapped: too short: 131335
Unmapped: other: 0