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.
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