I have problems seeing the output from STAR mapper. I have done the mapping, then made an sorted bam for IGV but I see very few reads mapped, and I have this log:
Number of input reads | 116876253 Average input read length | 20 UNIQUE READS: Uniquely mapped reads number | 93912191 Uniquely mapped reads % | 80.35% Average mapped length | 19.85 Number of splices: Total | 129488 Number of splices: Annotated (sjdb) | 0 Number of splices: GT/AG | 129455 Number of splices: GC/AG | 33 Number of splices: AT/AC | 0 Number of splices: Non-canonical | 0 Mismatch rate per base, % | 0.00% Deletion rate per base | 0.00% Deletion average length | 1.00 Insertion rate per base | 0.00% Insertion average length | 1.00 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 20734865 % of reads mapped to multiple loci | 17.74% Number of reads mapped to too many loci | 2072050 % of reads mapped to too many loci | 1.77% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.00% % of reads unmapped: other | 0.13%
I'm particularly interested to see the reads that are splitted in exon-intron sites:
Number of splices: GT/AG | 129455
I have noticed that when converting from SAM to BAM the size decreased from 16GB to only 60MB which is strange?!