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# look at a subset of field for chrI:1000-2000 reads # 2=flags, 3=contig, 4=start, 5=mapping quality, 6=CIGAR, 9=insert size samtools view -F 0x4 yeast_pe.sort.bam chrI:1000-2000 | cut -f 2-6,9 | \ awk ' BEGIN{FS=OFS="\t"}{$1 = sprintf("0x%x", $1); print}' |
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