STAR version=2.7.10a STAR compilation time,server,dir=2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source STAR git: On branch master ; commit ae26add7ea1724f3281ec8abedb71bcff6a4ae73 ; diff files: CHANGES.md README.md RELEASEnotes.md doc/STARmanual.pdf extras/doc-latex/STARmanual.tex extras/doc-latex/convertParDefT> Command Line: STAR --genomeDir genome_index --runThreadN 15 --readFilesIn fastp_output/SRR15881871_1_good.fq.gz fastp_output/SRR15881871_2_good.fq.gz --readFilesCommand zcat --outFileNamePrefix mapping/SRR15881871/SRR1588187> Initial USER parameters from Command Line: outFileNamePrefix mapping/SRR15881871/SRR15881871_ All USER parameters from Command Line: genomeDir genome_index ~RE-DEFINED runThreadN 15 ~RE-DEFINED readFilesIn fastp_output/SRR15881871_1_good.fq.gz fastp_output/SRR15881871_2_good.fq.gz ~RE-DEFINED readFilesCommand zcat ~RE-DEFINED outFileNamePrefix mapping/SRR15881871/SRR15881871_ ~RE-DEFINED outSAMtype BAM SortedByCoordinate ~RE-DEFINED outSAMstrandField intronMotif ~RE-DEFINED outSAMattributes All ~RE-DEFINED outFilterIntronMotifs RemoveNoncanonical ~RE-DEFINED Finished reading parameters from all sources Final user re-defined parameters-----------------: runThreadN 15 genomeDir genome_index readFilesIn fastp_output/SRR15881871_1_good.fq.gz fastp_output/SRR15881871_2_good.fq.gz readFilesCommand zcat outFileNamePrefix mapping/SRR15881871/SRR15881871_ outSAMtype BAM SortedByCoordinate outSAMstrandField intronMotif outSAMattributes All
Time Speed Read Read Mapped Mapped Mapped Mapped Unmapped Unmapped Unmapped Unmapped M/hr number length unique length MMrate multi multi+ MM short other Mar 29 21:36:51 189.6 3160425 199 85.7% 198.9 0.3% 12.5% 0.2% 0.0% 1.3% 0.2% Mar 29 21:37:55 214.4 7383400 199 85.7% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2% Mar 29 21:38:58 237.6 12340759 199 85.7% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2% Mar 29 21:39:59 243.6 16778478 199 85.7% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2% Mar 29 21:40:59 233.4 19966239 199 85.7% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2% Mar 29 21:42:01 222.2 22841274 199 85.6% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2% Mar 29 21:44:36 172.1 25095163 199 85.6% 198.8 0.3% 12.5% 0.2% 0.0% 1.4% 0.2%
Started job on | Mar 29 21:35:30 Started mapping on | Mar 29 21:35:51 Finished on | Mar 29 21:44:36 Mapping speed, Million of reads per hour | 172.08 Number of input reads | 25095163 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 21489980 Uniquely mapped reads % | 85.63% Average mapped length | 198.84 Number of splices: Total | 4482974 Number of splices: Annotated (sjdb) | 4414683 Number of splices: GT/AG | 4446804 Number of splices: GC/AG | 32461 Number of splices: AT/AC | 3709 Number of splices: Non-canonical | 0 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 1.82 Insertion rate per base | 0.01% Insertion average length | 1.45 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3149053 % of reads mapped to multiple loci | 12.55% Number of reads mapped to too many loci | 55833 % of reads mapped to too many loci | 0.22% UNMAPPED READS: Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 344611 % of reads unmapped: too short | 1.37% Number of reads unmapped: other | 55686 % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%
Note that STAR counts a paired-end read as one read(unlike the samtools flagstat/idxstats, which count each mate separately).
junction start/end
intronic bases
exonic bases
chr1 10060 10106 2 2 0 0 1 41 chr1 10060 10178 2 2 0 0 1 46 chr1 10066 10106 2 2 0 0 1 41 chr1 10066 10178 2 2 0 0 1 46 chr1 10072 10106 2 2 0 0 1 41 chr1 10072 10178 2 2 0 0 1 46 chr1 10078 10106 2 2 0 0 1 41 chr1 10078 10178 2 2 0 0 1 46 chr1 10084 10106 2 2 0 0 1 41