trouble loading the hic file in to Juicebox

[Vivek]

Hi all,

I have processed my fastq files using the juicer script and I tried to load the hic files in to the juicebox application. It does not seem to do anything. 

I tried to convert the hic files (using juicebox dump) to a txt file to take a look at it. It gives me the following error.

ubuntu@ip-10-87-154-174:~/juicer-master/AWS/scripts$ ./juicebox dump observed KR ~/data/test/aligned/inter.hic 1 1 BP 2500000 chr1_2.5MB.txt

HiC file version: 8

Could not read hic file: Index: 1, Size: 1

The merged_nodups.txt also looked different than what I downloaded from the GEO for the rao et al paper. Any suggestions would be very helpful!

Mine:

0 2L 376 3 16 2L 5142 34 0 76M GTATGCGAGAGTAGTGCCAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCACAAA 0 76M AGATATTTTGATTGCCTCTCATTTTCTCTCCAATATTATAGGTTGATATATGTTCGCGTATGCGAGAGTAGTGCCA NS500406:55:H3VGYAFXX:1:21108:6066:17323/1 NS500406:55:H3VGYAFXX:1:21108:6066:17323/2 

0 2L 389 3 16 2L 5123 34 0 76M GTGCCAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAAACCCAAATCGACAA 0 76M ACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCATTTTCTCTCCCATATTATAGGGTGAAATATGATCGC NS500406:55:H3VGYAFXX:1:21102:20972:16185/1 NS500406:55:H3VGYAFXX:1:21102:20972:16185/2 

Downloaded one:

D258GACXX130605:6:2303:11972:8990 0 1 10008 0 16 1 10108 0 0 0

D258GACXX130605:6:1215:17680:49478 0 1 10011 0 16 1 10390 0 0 1

D258GACXX130605:6:2206:15628:5426 0 1 10111 0 16 1 10128 0 0 0

D258GACXX130605:6:1202:7769:56983 16 1 10152 0 16 1 743008 1450 0 0

D258GACXX130605:6:2313:3646:14099 16 1 10108 0 16 1 110169728 283019 0 178

C24LCACXX130513:6:1202:9818:83079 16 1 10108 0 16 1 249125889 576087 0 178

Thank you very much

Vivek

[Neva Durand]

Hi Vivek,

The merged_nodups.txt file is fine; there are two different kinds and the pipeline produces the kind you see.  

Did you have any error messages when you ran the pipeline?

Also have a look at juicebox.log and post it here; juicebox.log should be in your default user directory.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Vivek]

Thanks for the reply Neva. I am now trying to run the commands in the AMI image provided by you guys.