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aidenlab / straw

Extract data quickly from Juicebox via straw
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Extract reads between non-consecutive bins #24

Open wgmao opened 6 years ago

wgmao commented 6 years ago

The examples (https://github.com/theaidenlab/straw/wiki/CPP#running) show how to extract reads between two consecutive regions on the chromosome. If I have two sets of bins which are not consecutive, and I am only interested to extract reads between these two sets of bins, is there a fast way to use straw to do that? Thanks.

nchernia commented 6 years ago

I am not sure I understand the question. You can extract reads that are off diagonal between different bins, e.g.:

straw KR HIC001.hic 1:1000000:7400000 1:2000000:8400000 BP 25000

On Thu, May 3, 2018 at 5:25 PM, wgmao notifications@github.com wrote:

The examples (https://github.com/theaidenlab/straw/wiki/CPP#running) show how to extract reads between two consecutive regions on the chromosome. If I have two sets of bins which are not consecutive, and I am only interested to extract reads between these two sets of bins, is there a fast way to use straw to do that? Thanks.

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wgmao commented 6 years ago

Sorry for the confusion. For example, I have two sets of bins:

Set1: 1:1000000:2000000 1:6000000:7400000

Set2: 1:2000000:3000000 1:7000000:8400000

If I would like to extract the reads between these two sets, I have to query four times. straw KR HIC001.hic 1:1000000:2000000 1:2000000:3000000 BP 25000 straw KR HIC001.hic 1:1000000:2000000 1:7000000:8400000 BP 25000 straw KR HIC001.hic 1:6000000:7400000 1:2000000:3000000 BP 25000 straw KR HIC001.hic 1:6000000:7400000 1:7000000:8400000 BP 25000

If I only query once: straw KR HIC001.hic 1:1000000:7400000 1:2000000:8400000 BP 25000 I have to filter a lot of regions which don't overlap with these two sets.

Querying four times externally is one solution but it can be painful if sets are really large. I just wonder if there is an internal way to extract reads given two sets of non-overlapping bins. Thanks a lot.