arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
140 stars 85 forks source link

BAM to BEDPE #127

Open hmyh1202 opened 6 years ago

hmyh1202 commented 6 years ago

Hi, I want to transform BAM(produced by Bowtie2) to BEDPE format. bam file was sorted by sequence names, and then do samtools view -f 0x2 -b test.srtn.bam | bamToBed -bedpe -i - > sortn.bam.bed. However, it was reported such as '*****WARNING: Query SRR5099535-74922/1 is marked as paired, but its mate does not occur^Z next to it in your BAM file. Skipping. .....', and with no results output.

My bedtools version is v2.20.1, and how can I solve it.

Thanks