HiCCUPS: 0 loops written to file

[Jing Wan]

Hi,

I used HiCCUPS to call loops. My test Hi-C data is GSM1551550. 

And this is my command:

java -jar ~/tools/juicebox/juicer_tools.1.7.5_linux_x64_jcuda.0.8.jar hiccups -m 2048 -r 10000 -k NONE inter_30.hic ../hiccups_res

But I got this result:

Reading file: inter_30.hic

HiC file version: 8

Using the following configurations for HiCCUPS:

Config res: 10000 peak: 2 window: 5 fdr: 10% radius: 20000

Running HiCCUPS for resolution 10000

0 loops written to file: ../hiccups_res/merged_loops

HiCCUPS complete

There is no loops in the results. Is my data too sparse? But I tested other data and got the same result.

why it would be this? How can I resolve this problem?

Thanks!

[Neva Durand]

Hello,

How sparse is the file (how many reads)?  I'm surprised you didn't run into the sparsity warning.  Also, why are you not using normalization?

GSM1551550 refers to this file:  http://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/HIC001_30.hic

When I run hiccups on it with your flags, I get:

Warning Hi-C map is too sparse to find many loops via HiCCUPS.

Exiting. To disable sparsity check, use the --ignore_sparsity flag.

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Jing Wan]

Hi Neva,

I used another data and --ignore_sparsity flag. And I got the same result: 0 loops written to file. 

And this is data information:

Sequenced Read Pairs:  143,287,205

 Normal Paired: 121,174,265 (84.57%)

 Chimeric Paired: 15,954,006 (11.13%)

 Chimeric Ambiguous: 3,871,840 (2.70%)

 Unmapped: 2,287,094 (1.60%)

 Ligation Motif Present: 58,749,828 (41.00%)

Alignable (Normal+Chimeric Paired): 137,128,271 (95.70%)

Unique Reads: 112,746,103 (78.69%)

PCR Duplicates: 23,515,855 (16.41%)

Optical Duplicates: 866,313 (0.60%)

Library Complexity Estimate: 347,919,826

Intra-fragment Reads: 26,576,169 (18.55% / 23.57%)

Below MAPQ Threshold: 23,527,144 (16.42% / 20.87%)

Hi-C Contacts: 62,642,790 (43.72% / 55.56%)

 Ligation Motif Present: 29,008,449  (20.24% / 25.73%)

 3' Bias (Long Range): 81% - 19%

 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%

Inter-chromosomal: 6,938,127  (4.84% / 6.15%)

Intra-chromosomal: 55,704,663  (38.88% / 49.41%)

Short Range (<20Kb): 31,760,458  (22.17% / 28.17%)

Long Range (>20Kb): 23,944,168  (16.71% / 21.24%)

Is data too sparse? How can I resolve it and make HiCCUPS run a normal result?

Thank you! 

[Neva Durand]

Yes, it’s an order of magnitude too few reads to find loops. You need to do deeper sequencing  / more replicates and then combine them. You need at least 1 billion reads. Otherwise your experiments simply don’t have the depth to determine loops (with any algorithm). 

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