Juicer completes with no errors, but no debug/ and no .hic files with intra-chromosomal reads created

[kalav...@gmail.com]

Dear Neva and Juicer crew,

I would like to ask your advice to troubleshoot this issue:

I am running the Juicer pipeline with the HIC003 R1 and R2 test data available at the Juicer wiki/Aiden lab Box mirror. The pipeline seems to complete without errors. However, no debug/ is generated, and the following output files are found in aligned/:

abnormal.sam

collisions.txt

dups.txt

inter_30_contact_domains.txt

inter_30_hists.m

inter_30_loops.txt

inter_30.hic

inter_30.txt

inter_hists.m

inter.hic

inter.txt

merged_nodups.txt

merged_sort.txt

opt_dups.txt

stats_dups_hists.m

stats_dups.txt

unmapped.sam

There seems to be an absence of .hic files containing intra-chromosomal reads.

I called juicer.sh with the -d and -s flags. I attached my lsf.out file.

Thank you for your willingness to help!

Kris

[Neva Durand]

This looks fine.  In general you can run "tail lsf.out" to check.  In this case, the very end of the your file says "(-: Pipeline successfully completed (-:" which is what you want to see.

We no longer have access to an LSF system so have no way to update the LSF script to be the same as the others; consequently some improvements haven't been ported (like the debug folder and threads option).  However, it should still work.  If you or anyone else wants to port over the updates to LSF, feel free to do so and create a pull request.

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Neva Durand]

Oh, and inter.hic / inter_30.hic contain all Hi-C contacts (intra and inter); just a funny naming convention.

[kalav...@gmail.com]

Thank you, Neva.

Somehow, when I load the inter.hic and inter_30.hic files generated from the HIC003 data into Juicebox, I see no intra-chromosomal contacts in the matrix. Is this normal for the HIC003 test data, which have a low number of reads compared to normal Hi-C experiments?

I attached a screenshot of Juicebox loaded with inter_30.hic.

Thanks again,

Kris

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Neva Durand]

The statistics are strange / incorrect and the map is incorrect.  It looks like many of your reads were classified as intra-fragment.  Look at the first few lines of merged_nodups.txt.  Are the chr and frag the same for read1 and read2?  What did you use for hg19_MboI.txt ?

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[kalav...@gmail.com]

Thank you, Neva. The problem was with the hg19_MboI.txt file, which became corrupted. I ran the pipeline with a good hg19_MboI.txt file, and now it's fine. Thanks for all of your help!

-Kris

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