gravatar for MJ

2 hours ago by

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

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2 hours ago
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MJ0



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