convert bam to bed need sort

[YFan1997]

Dear Dr. Zheng,

I found this step on 4.2 may need an additional step needed for mapped bam file : sorting by samtools sort -n
otherwise, bed file is not comprehensive

Convert into bed file format

bedtools bamtobed -i $projPath/alignment/bam/${histName}_bowtie2.mapped.bam -bedpe >$projPath/alignment/bed/${histName}_bowtie2.bed

Best and thank you,
Yifan

[xinghui-guo]

Yes!