91 lines
3.0 KiB
Bash
91 lines
3.0 KiB
Bash
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# echo processing raw reads with fastp
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# pancancer_singlesample boold
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fastp \
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-i /dataseq/T7/result/OutputFq/upload/E150013722/L01/*_JM-181200004530_*1.fq.gz \
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-o /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530_clean_R1.fq.gz \
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-I /dataseq/T7/result/OutputFq/upload/E150013722/L01/*_JM-181200004530_*2.fq.gz \
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-O /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530_clean_R2.fq.gz \
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-j /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530.json \
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-h /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530.html \
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--disable_trim_poly_g \
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--disable_quality_filtering \
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-w 10 \
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--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
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--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
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--report_title JM-181200004530
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# singlecancer_singlesample_umi boold
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fastp \
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-i ${inputDir}/*_${tumor}_*1.fq.gz \
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-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
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-I ${inputDir}/*_${tumor}_*2.fq.gz \
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-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
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-j ${outputDir}/qc/${tumor}.json \
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-h ${outputDir}/qc/${tumor}.html --report_title ${tumor}\
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-w 10 \
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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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# comcancer_singelsample_cfDNA
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# 替换头部
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sekit ...
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fastp -i ${outputDir}/qc/${tumor}_changehead_R1.fq \
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-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
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-I ${outputDir}/qc/${tumor}_changehead_R2.fq \
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-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
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-w 10 \
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-U --umi_loc=per_read \
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--umi_len=4 \
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--umi_prefix=UMI \
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--umi_skip=3 \
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--disable_trim_poly_g \
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--correction \
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--overlap_len_require 10 \
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-j ${outputDir}/qc/${tumor}.json \
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-h ${outputDir}/qc/${tumor}.html \
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--report_title ${tumor} -e 20
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# UMI
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python3 ${codes_dir}/UMI_Project.py -i ${inputDir} -o ${outputDir} -t ${tumor}
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rm ${outputDir}/qc/${tumor}_changehead_R1.fq ${outputDir}/qc/${tumor}_changehead_R2.fq
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# 624
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fastp -i ${outputDir}/qc/${tumor}_changehead_R1.fq \
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-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
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-I ${outputDir}/qc/${tumor}_changehead_R2.fq \
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-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
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-w 10 \
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-U \
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--umi_loc=per_read \
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--umi_len=4\
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--umi_prefix=UMI\
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--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 ${outputDir}/qc/${tumor}.json \
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-h ${outputDir}/qc/${tumor}.html --report_title ${tumor}
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# UMI
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python3 ${codes_dir}/UMI_Project.py -i ${inputDir} -o ${outputDir} -t ${tumor}
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rm ${outputDir}/qc/${tumor}_changehead_R1.fq ${outputDir}/qc/${tumor}_changehead_R2.fq
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# 682
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fastp \
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-i ${inputDir}/*_${name}_*1.fq.gz \
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-o ${outputDir}/qc/${name}_clean_R1.fq.gz \
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-I ${inputDir}/*_${name}_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
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-w 10 \
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--correction \
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--overlap_len_require 10 \
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-j ${outputDir}/qc/${name}.json \
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-h ${outputDir}/qc/${name}.html \
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--report_title ${name} \
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-e 20
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