hicpro2juicebox.sh: Could not find chromosome sizes file for: susScr3

[Sarah Djebali]

Dear all,

I am trying to visualize hicpro results in juicebox for the pig genome.

For this I converted the hicpro output into a format that juicebox can read following the instructions here:

https://github.com/nservant/HiC-Pro/blob/master/doc/UTILS.rst

After installing the juicebox command line tools, I did the following:

module load bioinfo/Java8
/work2/project/fragencode/tools/hicpro/HiC-Pro_2.7.7/bin/utils/hicpro2juicebox.sh -i ~/fragencode/results/hic/sus_scrofa/testrun20160422.v2.7.7/Pig1/hicpro/output/hic_results/data/liver/liver_allValidPairs -g susScr3 -r /work2/project/fragencode/data/species/sus_scrofa/Sscrofa10.2.84/restrictionfragments_HindIII.bed -j /usr/local/bioinfo/src/Juicebox/juicebox-1.4/out/artifacts/Juicebox_clt_jar/Juicebox.jar

and I got the following error message:
Could not find chromosome sizes file for: susScr3

I also tried with the -c option but it gave me the same error.

Do you know how I can pass the chromosome size file for this genome?

Best regards,
Sarah Djebali

[Neva Durand]

Hi Sarah,

We suggest using our pipeline, Juicer, for creating Hi-C maps.  There's a lot of documentation on it here:

http://aidenlab.org/juicer/

If you have already created a paired read file, you can use the Juicebox command line tools:

http://aidenlab.org/juicebox/docs.html

Scroll down and click the tab for Command Line Tools, then Creating a Hi-C File.  

To use a genome that hasn't yet been included in the standard distribution, simply use UCSC's chrom.sizes file in place of the genome ID.  See the previous thread:  

https://groups.google.com/forum/embed/?place=forum/3d-genomics&showsearch=true&showpopout=true&parenturl=http%3A%2F%2Faidenlab.org%2Fforum.html#!topic/3d-genomics/uH0uOw6gV_c

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Lila Rieber]

You need to have the S scrofa chromosome sizes file in the same directory as the reference genome. The format of the file name must be [reference genome name].chrom.sizes. For example, if your reference genome is in ../references/s_scrofa.fasta, the sizes file must be ../references/s_scrofa.fasta.chrom.sizes. Here's the file format for the human genome: https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes.  I don't know of a file of this for S scrofa, but you could make it manually.