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hammerlab / pileup.js

Interactive in-browser track viewer
Apache License 2.0
274 stars 64 forks source link

community contributed plugin track #536

Open Parul-Kudtarkar opened 4 years ago

Parul-Kudtarkar commented 4 years ago

Hi!

How easy/seamless is it to add community contributed plugin track? Are there any examples/demonstrations available?

Thanks, Parul

akmorrow13 commented 4 years ago

Hi @Parul-Kudtarkar,

We are very open to community contributions! What particular type of track are you interested in adding?

Parul-Kudtarkar commented 4 years ago

Hi @akmorrow13, Thanks for confirming! I am thinking of chromatin interactions

akmorrow13 commented 4 years ago

Yes that would be excellent! @Parul-Kudtarkar what file types store chromatin interactions?

Parul-Kudtarkar commented 4 years ago

I am thinking ChIA-PET or Capture Hi-C in .bed format.

akmorrow13 commented 4 years ago

Ok. The .bed format may be easiest. We currently do not have a DataSource for bed or ChIA-PET. We do, however, support bigbed files. We have been meaning to add bed support for a while but have not yet done it. It should be easy to implement given there is no compression.

Parul-Kudtarkar commented 4 years ago

Do you know when the bed format support will be added? Is there anything I can do to assist? Thank you very much!

akmorrow13 commented 4 years ago

Unfortunately due to loss of man power adding bed support has completely dropped off the table because we already support bigbed files. However, if you can implement the chromatin interaction Visualization Track via a bigbed file, I can then look into adding a bed format to be used by the chromatin interaction visualization. To do this, you can start by copying code for the Feature Track, which can read features similar to what you would see in a bed file.

Parul-Kudtarkar commented 4 years ago

Excellent! Thank you so much @akmorrow13 I will keep you posted