#!/bin/bash

#
seqkit replace -p "/1" -r " 1" -j 10 /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803_*1.fq.gz \
-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq

seqkit replace -p "/2" -r " 2" -j 10 /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803_*2.fq.gz \
-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq

#
fastp -i /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq \
-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_clean_R1.fq.gz \
-I /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq \
-O /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_clean_R2.fq.gz \
-w 10 -U --umi_loc=per_read --umi_len=4 --umi_prefix=UMI --umi_skip=3 \
--disable_trim_poly_g \
--disable_quality_filtering \
--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
--correction \
--overlap_len_require 10 \
-j /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803.json \
-h /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803.html --report_title PQSK-20230803
# UMI
python3 /dataseq/jmdna/codes/624/UMI_Project.py \
-i /dataseq/T7/result/OutputFq/upload/E100076595/L01 \
-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803 \
-t PQSK-20230803

rm /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R1.fq \
/home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803_changehead_R2.fq

# 对照样本
fastp -i /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803-B_*1.fq.gz \
-o /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B_clean_R1.fq.gz \
-I /dataseq/T7/result/OutputFq/upload/E100076595/L01/*_PQSK-20230803-B_*2.fq.gz \
-O /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B_clean_R2.fq.gz \
-w 10 --correction --overlap_len_require 20 \
--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
-j /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B.json \
-h /home/jm001/project/pancancer_controlsample/624/Blood/PQSK-20230803/qc/PQSK-20230803-B.html --report_title PQSK-20230803-B -e 20