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Copy pathflexbar_batch.sh
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Copy pathflexbar_batch.sh
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executable file
·9 lines (9 loc) · 1.61 KB
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zcat tmp/x00.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x00.exp_barcodes.detected
zcat tmp/x01.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x01.exp_barcodes.detected
zcat tmp/x02.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x02.exp_barcodes.detected
zcat tmp/x03.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x03.exp_barcodes.detected
zcat tmp/x04.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x04.exp_barcodes.detected
zcat tmp/x05.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x05.exp_barcodes.detected
zcat tmp/x06.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x06.exp_barcodes.detected
zcat tmp/x07.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x07.exp_barcodes.detected
zcat tmp/x08.fastq.gz | awk -v umi1_len=5 -v exp_bc_len=6 '{ if (FNR%4==2) print substr($1,(umi1_len+1),exp_bc_len) }' | sort | uniq -c | sort -k1,1rn > tmp/x08.exp_barcodes.detected