Hi，all It was the first time for me to map RNA sequence. The data generated from corals .I used STAR to map the sequence to the reference. I used the default parameter but got a terrible result. The final mapping result was
Started job on | Dec 12 16:02:44 Started mapping on | Dec 12 16:03:13 Finished on | Dec 12 16:12:34 Mapping speed, Million of reads per hour | 85.99 Number of input reads | 13400813 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 3114 Uniquely mapped reads % | 0.02% Average mapped length | 124.34 Number of splices: Total | 41 Number of splices: Annotated (sjdb) | 2 Number of splices: GT/AG | 24 Number of splices: GC/AG | 4 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 13 Mismatch rate per base, % | 4.13% Deletion rate per base | 0.03% Deletion average length | 1.86 Insertion rate per base | 0.01% Insertion average length | 1.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1505 % of reads mapped to multiple loci | 0.01% Number of reads mapped to too many loci | 47 % of reads mapped to too many loci | 0.00% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 99.96% % of reads unmapped: other | 0.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
Is there any idea about the too many unmapped reads? I didn't understand what the reason 'too short' mean. Can somebody explain it？Thanks!