FastQ test data cannot be aligned

[Redmar-van-den-Berg]

I'm trying to use the FastQ files from https://github.com/suhrig/arriba/tree/master/test with STAR, but all of the reads are unmapped:

                          Number of input reads |   40
                      Average input read length |   300
                                    UNIQUE READS:
                   Uniquely mapped reads number |   0
                        Uniquely mapped reads % |   0.00%
                          Average mapped length |   0.00
                       Number of splices: Total |   0
            Number of splices: Annotated (sjdb) |   0
                       Number of splices: GT/AG |   0
                       Number of splices: GC/AG |   0
                       Number of splices: AT/AC |   0
               Number of splices: Non-canonical |   0
                      Mismatch rate per base, % |   -nan%
                         Deletion rate per base |   0.00%
                        Deletion average length |   0.00
                        Insertion rate per base |   0.00%
                       Insertion average length |   0.00
                             MULTI-MAPPING READS:
        Number of reads mapped to multiple loci |   0
             % of reads mapped to multiple loci |   0.00%
        Number of reads mapped to too many loci |   0
             % of reads mapped to too many loci |   0.00%
                                  UNMAPPED READS:
  Number of reads unmapped: too many mismatches |   0
       % of reads unmapped: too many mismatches |   0.00%
            Number of reads unmapped: too short |   0
                 % of reads unmapped: too short |   0.00%
                Number of reads unmapped: other |   40
                     % of reads unmapped: other |   100.00%
                                  CHIMERIC READS:
                       Number of chimeric reads |   0
                            % of chimeric reads |   0.00%

[suhrig]

What command did you use to do the alignment?

[Redmar-van-den-Berg]

@suhrig I was running against a reduced reference that didn't include all chromosomes, hence the unmapped reads. Against the full reference, I do get the fusion back!