community contributed plugin track

[Parul-Kudtarkar]

Hi!

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

Thanks, Parul

[akmorrow13]

Hi @Parul-Kudtarkar,

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

[Parul-Kudtarkar]

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

[akmorrow13]

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

[Parul-Kudtarkar]

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

[akmorrow13]

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]

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

[akmorrow13]

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]

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