Mapping RNA-seq Reads with STAR
最后发布时间:2022-04-02 10:14:43
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Output files
- Log.out: 主日志文件，包含大量有关运行的详细信息，此文件对于故障排除和调试非常有用。
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
- Log.progress.out：报告job进度统计信息，如已处理reads的数量、mapped reads的百分比等。每隔1分钟更新一次。
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%
- Log.final.out：绘图工作完成后的绘图统计摘要，对质量控制非常有用。
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).
- SJ.out.tab
每个拼接都以拼接数计算，这将对应于以SJ求和的计数
SJ.out.tab 包含制表符分隔格式的高置信度折叠拼接接头。请注意，Star将junction start/end点定义为intronic bases，而许多其他软件将其定义为exonic bases。这些列具有以下含义： - column 1: chromosome
- column 2: first base of the intron (1-based)
- column 3: last base of the intron (1-based)
- column 4: strand (0: undefined, 1: +, 2: -)
- column 5: intron motif: 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT
- column 6: 0: unannotated, 1: annotated in the splice junctions database. Note that in 2-pass mode, junctions detected in the 1st pass are reported as annotated, in addition to annotated junctions from GTF.
- column 7: number of uniquely mapping reads crossing the junction
- column 8: number of multi-mapping reads crossing the junction
- column 9: maximum spliced alignment overhang
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
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