commands
/Share/home/zhangqf/lipan/usr/icSHAPE-pipe-1.0.0/bin/Functions/readDistributionStatistic.py -@ /Share/home/zhangqf8/zhuoer/raw/GSE45803/SRR815612.fastq.gz,1.uniqReads/yeast_vivo_rep1.fq,2.trimReads/yeast_vivo_rep1.fq.gz,3.rem_rRNA/yeast_vivo_rep1.fq,4.map_smallRNA/yeast_vivo_rep1.fq,5.map_genome/yeast_vivo_rep1.sorted.bam -@ /Share/home/zhangqf8/zhuoer/raw/GSE45803/SRR815613.fastq.gz,1.uniqReads/yeast_vivo_rep2.fq,2.trimReads/yeast_vivo_rep2.fq.gz,3.rem_rRNA/yeast_vivo_rep2.fq,4.map_smallRNA/yeast_vivo_rep2.fq,5.map_genome/yeast_vivo_rep2.sorted.bam -@ /Share/home/zhangqf8/zhuoer/raw/GSE45803/SRR815614.fastq.gz,1.uniqReads/yeast_vivo_rep3.fq,2.trimReads/yeast_vivo_rep3.fq.gz,3.rem_rRNA/yeast_vivo_rep3.fq,4.map_smallRNA/yeast_vivo_rep3.fq,5.map_genome/yeast_vivo_rep3.sorted.bam -@ /Share/home/zhangqf8/zhuoer/raw/GSE45803/SRR815615.fastq.gz,1.uniqReads/yeast_vivo_rep4_1.fq,2.trimReads/yeast_vivo_rep4_1.fq.gz,3.rem_rRNA/yeast_vivo_rep4_1.fq,4.map_smallRNA/yeast_vivo_rep4_1.fq,5.map_genome/yeast_vivo_rep4_1.sorted.bam -@ /Share/home/zhangqf8/zhuoer/raw/GSE45803/SRR815616.fastq.gz,1.uniqReads/yeast_vivo_rep4_2.fq,2.trimReads/yeast_vivo_rep4_2.fq.gz,3.rem_rRNA/yeast_vivo_rep4_2.fq,4.map_smallRNA/yeast_vivo_rep4_2.fq,5.map_genome/yeast_vivo_rep4_2.sorted.bam --processtag raw,unique,trimmed,map_rRNA,smallRNA,mapGenome --sampletag yeast_vivo_rep1,yeast_vivo_rep2,yeast_vivo_rep3,yeast_vivo_rep4_1,yeast_vivo_rep4_2 -o readDistribution/yeast_vivo
The figure below shows the number of remaining reads for each processing step.
| Sample name | raw | unique | trimmed | map_rRNA | smallRNA | mapGenome | un-mapped |
|---|---|---|---|---|---|---|---|
| yeast_vivo_rep1 | 172,245,327 (100.00%) | 44,740,810 (25.98%) | 42,129,336 (24.46%) | 37,787,600 (21.94%) | 37,621,984 (21.84%) | 34,415,398 (19.98%) | 3,206,586 (1.86%) |
| yeast_vivo_rep2 | 58,412,618 (100.00%) | 21,273,281 (36.42%) | 17,166,144 (29.39%) | 15,528,924 (26.58%) | 15,475,229 (26.49%) | 13,789,034 (23.61%) | 1,686,195 (2.89%) |
| yeast_vivo_rep3 | 210,882,033 (100.00%) | 42,535,758 (20.17%) | 34,712,849 (16.46%) | 32,336,453 (15.33%) | 32,237,397 (15.29%) | 29,519,794 (14.00%) | 2,717,603 (1.29%) |
| yeast_vivo_rep4_1 | 179,038,246 (100.00%) | 43,845,058 (24.49%) | 40,654,971 (22.71%) | 37,404,001 (20.89%) | 37,251,840 (20.81%) | 34,536,686 (19.29%) | 2,715,154 (1.52%) |
| yeast_vivo_rep4_2 | 105,355,630 (100.00%) | 31,244,246 (29.66%) | 29,146,987 (27.67%) | 25,879,163 (24.56%) | 25,751,669 (24.44%) | 23,571,765 (22.37%) | 2,179,904 (2.07%) |