I used STAR to map my RNA seq data to the genome, here is the output file for the mapping rate, but I had a hard time to understand it..
Started job on | Aug 09 16:35:19 Started mapping on | Aug 09 16:35:48 Finished on | Aug 09 17:28:18 Mapping speed, Million of reads per hour | 21.41 Number of input reads | 18734806 Average input read length | 249 UNIQUE READS: Uniquely mapped reads number | 10373363 Uniquely mapped reads % | 55.37% Average mapped length | 242.88 Number of splices: Total | 8480091 Number of splices: Annotated (sjdb) | 7969501 Number of splices: GT/AG | 8357360 Number of splices: GC/AG | 77588 Number of splices: AT/AC | 6734 Number of splices: Non-canonical | 38409 Mismatch rate per base, % | 0.28% Deletion rate per base | 0.03% Deletion average length | 2.76 Insertion rate per base | 0.02% Insertion average length | 2.49 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1489776 % of reads mapped to multiple loci | 7.95% Number of reads mapped to too many loci | 6179 % of reads mapped to too many loci | 0.03% UNMAPPED READS: Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 6856355 % of reads unmapped: too short | 36.60% Number of reads unmapped: other | 9133 % of reads unmapped: other | 0.05% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
I just want to know if the mapping rate is
Uniquely mapped reads % (55.37%)
? Because when I used Hisat2, the mapping rate is the add for several things....So in here, if I use STAR..if I need to add some of the number?