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aidenlab / juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
http://aidenlab.org
MIT License
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Calculate map resolution #213

Closed Jssmith91 closed 2 years ago

Jssmith91 commented 3 years ago

Calculate map resolution gives the following after running on merged_no_dups.txt generated using juicer.

.../calculate_map_resolution.sh: line 104: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected

The map resolution is 100

Not sure how to fix this.

nchernia commented 3 years ago

Did you call it with two arguments?

On Thu, Mar 18, 2021 at 3:29 PM Jssmith91 @.***> wrote:

Calculate map resolution gives the following after running on merged_no_dups.txt generated using juicer.

.../calculate_map_resolution.sh: line 104: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected ../calculate_map_resolution.sh: line 153: [: -lt: unary operator expected

The map resolution is 100

Not sure how to fix this.

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

Jssmith91 commented 3 years ago

have been running ./calculate_map_resolution.sh path_to_merged_no_dups.txt 50bp.txt

nchernia commented 3 years ago

Was 50bp.txt written to?

On Thu, Mar 18, 2021 at 4:43 PM Jssmith91 @.***> wrote:

have been running ./calculate_map_resolution.sh path_to_merged_no_dups.txt 50bp.txt

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Jssmith91 commented 3 years ago

no the files are empty each time

nchernia commented 3 years ago

Your merged_nodups has enough fields?

On Thu, Mar 18, 2021 at 4:45 PM Jssmith91 @.***> wrote:

no the files are empty each time

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Jssmith91 commented 3 years ago

It has 16.

nchernia commented 3 years ago

Sorry for the late reply. Deleting all the empty files and starting over - does it break?

It seems that it's skipping over creating the 50bp vector, and I'm not sure why.

On Thu, Mar 18, 2021 at 4:48 PM Jssmith91 @.***> wrote:

It has 15.

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sa501428 commented 2 years ago

Was this resolved?

hermanzhaozzzz commented 1 year ago

He used a valid_pairs file generated by Hi-C Pro