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BAM to Bedgraph creating an empty file

Hi,

I downloaded a fastq file from a paper and was trying to create a Bedgraph file.

After mapping using bismark, I got a 12Gb bam file. And after deduplication, I used bismark_methylation_extractor to create the bedgraph file. There was no error but the Bedgraph file was only 40b and showed nothing. Also, thousands of temp files were created but not deleted.

Here is my code:

bismark --non_directional --genome ref/ trim/filename_trimmed.fq --multicore 2 -o map/
deduplicate_bismark --bam map/filename_trimmed_bismark_bt2.bam 
bismark_methylation_extractor --gzip --bedGraph filename_trimmed_bismark_bt2.deduplicated.bam

Could someone help me please?

bisulfite-seq bismark
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updated by hpf0210 • hpf0210 • written by irebekah.c • irebekah.c

You have a space in your reference path. Not sure it's intended?

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written by raphael.B • raphael.B

Hi, Thank you for replying. I have about 2.5TB free space there and I think that is enough? And I also tried with mapped-only reads or limited multicore but it doesn’t work anyway.

This is how it reported:

Now writing methylation information for file >>filename.deduplicated.mapped.txt.gz<< to individual files for each chromosome

Failed to open filehandle: Too many open files at /usr/local/bin/bismark2bedGraph line 278, <IN> line 44246607. Finished BedGraph conversion ...

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written by irebekah.c • irebekah.c

1 answer

Hi irebekah.c there is an issue on github about this p issue311,this is because your reference genome has genom with too many contigsscaffolds.

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written by hpf0210 • hpf0210

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