Hi all, while looking at my
log.final.out file, it dawned on me that my uniquely mapped reads is really low.
Mapping speed, Million of reads per hour | 113.33 Number of input reads | 11050047 Average input read length | 300 UNIQUE READS: Uniquely mapped reads number | 24100 Uniquely mapped reads % | 0.22% Average mapped length | 279.06 Number of splices: Total | 31927 Number of splices: Annotated (sjdb) | 6179 Number of splices: GT/AG | 11720 Number of splices: GC/AG | 315 Number of splices: AT/AC | 119 Number of splices: Non-canonical | 19773 Mismatch rate per base, % | 1.65% Deletion rate per base | 0.02% Deletion average length | 3.24 Insertion rate per base | 0.02% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 16802 % of reads mapped to multiple loci | 0.15% Number of reads mapped to too many loci | 630 % of reads mapped to too many loci | 0.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 99.61% % of reads unmapped: other | 0.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
I used STAR to make an index and subsequently aligned it. My command for STAR is as follow
STAR --genomeDir /home/user/scratch60/hg38_index \ --runThreadN 6 \ --readFilesIn /home/user/scratch60/SRR7059136.fastq \ --outFileNamePrefix /home/user/scratch60/STARresults/SRR7059136 \ --outSAMtype BAM SortedByCoordinate \ --outSAMunmapped Within \ --outSAMattributes Standard
If some one could shed some light onto this, that would be much appreciated. Thanks!