Error: the chromosome combination 7_7 appears in multiple blocks

[Paul Munn]

This is an error that doesn't seem to have been posted here before.

I'm attempting to run juicebox pre to convert a contact matrix for Drosophila into a .hic file.  Here are the first few lines of my file:

1000000 1 chr3R 7453812 2070 0 chr3R 6979042 1949 60 60

1000001 1 chr3R 10519580 2936 1 chr3R 10554865 2944 60 60

1000003 1 chr3R 25918719 7064 0 chr3R 25918602 7064 60 60

1000004 1 chr3R 14724784 4100 0 chr3R 14804702 4116 60 60

1000005 1 chrX 1929734 510 0 chrX 1929509 510 60 60

1000006 1 chr2L 19535945 5568 0 chr2L 19535786 5568 60 60

1000007 0 chrX 5949650 1429 0 chrX 11471779 2729 60 60

1000008 1 chr3R 4847811 1390 1 chr3R 11851735 3335 60 60

1000011 1 chr2R 1393932 617 0 chr2L 11850942 3229 60 60

1000014 0 chr3R 13133563 3643 1 chr3R 13107702 3635 60 60

And here's the command I'm using:

juicebox pre -q 1 ${hifive_file_path} $outputdir/test_output.hic ${juiceDir}/references/dm3.chrom.sizes

Any help appreciated,

Paul

[Neva Durand]

Hello Paul,

Actually it has, here: http://www.aidenlab.org/forum.html?place=msg%2F3d-genomics%2FbPAm69WEXVg%2F9_o_RcdrBAAJ

Unfortunately our documentation is still lacking - we are working on an overhaul.

You will need
1 - for the first read end chromosome to be less than the second read end chromosome; and
2 - for the reads to be sorted by chromosome block. That is, all chr3R-chr3R reads together in one place. This is so we don’t have to read the file multiple times.

To satisfy #1, do something like:

awk '{if ($3 > $7){ print $1, $6, $7, $8, $9, $11, $2, $3, $4, $5, $10}else {print}}' input.txt > input2.txt

Once you’ve ensured #1, you can do a command like

sort -k3,3d -k7,7d input2.txt > output.txt

to satisfy #2.

Best
Neva

​

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Paul Munn]

Thanks!  That worked great...