Hi, I had performed RNA-seq alignment using STAR for the sample Solanum tuberosum . I didn't understand the parameter "Number of splices: Annotated (sjdb)" and as it is zero for my sample I am pretty much worried if the gff file is used or not during analysis. Can anyone give me an explanation on this parameter? For reference I have attached the Alignment stats below.
Started mapping on | Apr 21 17:22:19
Finished on | Apr 21 17:28:05
Mapping speed, Million of reads per hour | 151.85
Number of input reads | 14594080
Average input read length | 298
UNIQUE READS:
Uniquely mapped reads number | 12744712
Uniquely mapped reads % | 87.33%
Average mapped length | 294.75
Number of splices: Total | 12412944
Number of splices: Annotated (sjdb) | 0
Number of splices: GT/AG | 12183896
Number of splices: GC/AG | 113682
Number of splices: AT/AC | 3944
Number of splices: Non-canonical | 111422
Mismatch rate per base, % | 0.91%
Deletion rate per base | 0.06%
Deletion average length | 2.90
Insertion rate per base | 0.05%
Insertion average length | 3.01
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 1364700
% of reads mapped to multiple loci | 9.35%
Number of reads mapped to too many loci | 98772
% of reads mapped to too many loci | 0.68%
UNMAPPED READS:
Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 383412 % of reads unmapped: too short | 2.63% Number of reads unmapped: other | 2484 % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
