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%