Hello, I know this is kinda question the forum has been tired of. I tried all the ideas suggested by you guys in similar threads, still cannot solved the problem. So I posted here again, hopefully someone can help me to fix it. I tried to convert the bam file of ChIP-seq pair-end to bedpe, but met error: "......is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.". Tried to sort, fixmate, resort, however, still have this error. Here are some command lines:
bamToBed -i test.sorted.bam | head -4
chr2 98507279 98507379 SRR40222.1.1/1 2 -
chr2 98506920 98507016 SRR40222.1.2/2 2 +
chr7 118889021 118889121 SRR40222.7.1/1 24 +
chr7 118889191 118889291 SRR40222.7.2/2 24 -
bamToBed -i test.sorted.bam -bedpe | head -4
*****WARNING: Query SRR40222.1.1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query SRR40222.1.2 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query SRR40222.3.1 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
*****WARNING: Query SRR40222.3.2 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.
It seems the reads are definitely paired, however, the /1 and /2 were ignored.
Thanks, MJ
You should name sort the BAM file.
That will bring mates next to each other on consecutive lines.
Thanks for your reply. The original bam file is already name sorted. I resorted it though, it still says the same error.
Can anyone see anything wrong? Thanks!
Perhaps try
bam2bed --split