45 lines
2.5 KiB
Bash
45 lines
2.5 KiB
Bash
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#!/bin/bash
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#
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seqkit replace -p "/1" -r " 1" -j 10 /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803_*1.fq.gz \
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-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq
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seqkit replace -p "/2" -r " 2" -j 10 /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803_*2.fq.gz \
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-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq
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#
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fastp -i /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq \
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-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_clean_R1.fq.gz \
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-I /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq \
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-O /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_clean_R2.fq.gz \
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-w 10 -U --umi_loc=per_read --umi_len=4 --umi_prefix=UMI --umi_skip=3 \
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--disable_trim_poly_g \
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--disable_quality_filtering \
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--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
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--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
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--correction \
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--overlap_len_require 10 \
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-j /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803.json \
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-h /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803.html --report_title PQSK-20230803
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# UMI
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python3 /dataseq/jmdna/codes/624/UMI_Project.py \
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-i /dataseq/T7/result/OutputFq/upload/E100076595/L01 \
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-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803 \
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-t PQSK-20230803
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rm /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq \
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/home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq
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# 对照样本
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fastp -i /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803-B_*1.fq.gz \
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-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B_clean_R1.fq.gz \
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-I /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803-B_*2.fq.gz \
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-O /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B_clean_R2.fq.gz \
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-w 10 --correction --overlap_len_require 20 \
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--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
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--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
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-j /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B.json \
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-h /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B.html --report_title PQSK-20230803-B -e 20
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