Possible issue with restriction fragment assignment or sam_to_pre script

[DustinSokolowski]

Hey Neva!

I hope that you're doing well! I've been having some issues with using 3d-DNA to complete a de novo diploid genome when I combine biological replicates. I've tried at the fastq level (with cat), the sam level (samtools), and the merged_nodups.txt level (mega).

I mentioned it to Olga as I originally thought it was an issue with 3d-DNA's compatibility (see full message below) and she thought that it may have to do with the restriction fragment assignment. Up to this point, I've been using "none" to generate restriction sites as I had a custom set of RE's and to this point, using "none" hasn't given me any trouble. I was wondering if you've had issues with using "none" for the RE's for juicer or perhaps if converting the sam file to mnd file can have issues when going into 3dDNA? In the mean time I'll work on getting a site positions file with the new genome.

Please see the full report below:

https://github.com/aidenlab/3d-dna/issues/132

Thanks so much! Dustin

[nchernia]

If you’re using none as the restriction enzyme I don’t know what you’d see this problem.

Olga I seem to remember another issue that caused empty blocks like this and we thought it was duplicates but it was not.

On Tue, Sep 28, 2021 at 10:51 AM Dustin Sokolowski @.***> wrote:

Hey Neva!

I hope that you're doing well! I've been having some issues with using 3d-DNA to complete a de novo diploid genome when I combine biological replicates. I've tried at the fastq level (with cat), the sam level (samtools), and the merged_nodups.txt level (mega).

I mentioned it to Olga as I originally thought it was an issue with 3d-DNA's compatibility (see full message below) and she thought that it may have to do with the restriction fragment assignment. Up to this point, I've been using "none" to generate restriction sites as I had a custom set of RE's and to this point, using "none" hasn't given me any trouble. I was wondering if you've had issues with using "none" for the RE's for juicer or perhaps if converting the sam file to mnd file can have issues when going into 3dDNA? In the mean time I'll work on getting a site positions file with the new genome.

Please see the full report below:

aidenlab/3d-dna#132 https://github.com/aidenlab/3d-dna/issues/132

Thanks so much! Dustin

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Senior Scientist | Gene Regulation Observatory Broad Institute of MIT and Harvard

[DustinSokolowski]

Hey Neva!

I re-aligned the Hi-C file to an earlier version of the assembly ( after I assembled with Flye instead of after I used Scaff10X). I'm not certain if I came across this error last time (because I deleted the stderr like an idiot) but I do see a java memory error. It shows up again a little later as well. My best guess is that it comes from "juicebox_tools.sh" in "/20210216/visualize/juicebox_tools.sh".

java -Xms49152m -Xmx49152m -jardirname $0/juicebox_tools.jar $*

One option I could try is to just crank the allocated memory up to what I my system can allow but before changing hard-coded parameters around I was wondering if you or Olga had seen this before and if there's something else I'll need to change?

Thanks so much! Dustin