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Hi,
I m running bamToBed using bedtools/2.18.0.
When I use the -bedpe option, I am getting an incomplete file, in particular, of my total 50 million reads (25M pairs), I am only getting ~400 000 in the bedpe file.
I want to ask for some advice about how to solve this problem.
I have tried
1) increasing the allocated memory for the process
2) checked whether I have both reads beloning to each pair in my bam file (I do)
3) omitting the -bedpe option, I get the correct bed file with 50 million reads in it
4) i looked at the location in the -n sorted bam where the writing stops, and I could not find any pattern to explain my observation
Thank you
I m running bamToBed using bedtools/2.18.0.
When I use the -bedpe option, I am getting an incomplete file, in particular, of my total 50 million reads (25M pairs), I am only getting ~400 000 in the bedpe file.
I want to ask for some advice about how to solve this problem.
I have tried
1) increasing the allocated memory for the process
2) checked whether I have both reads beloning to each pair in my bam file (I do)
3) omitting the -bedpe option, I get the correct bed file with 50 million reads in it
4) i looked at the location in the -n sorted bam where the writing stops, and I could not find any pattern to explain my observation
Thank you
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