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pkerpedjiev / negspy

Python NGS Repository
MIT License
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added galGal6 - contigs are gone #5

Closed sergpolly closed 5 years ago

sergpolly commented 5 years ago

working on this https://github.com/pkerpedjiev/negspy/issues/4 we ordered chroms as in galGal5 using little bash script https://docs.higlass.io/data_preparation.html#ordering-the-chromosomes-in-the-input-file the only problem is that all of the unassigned contigs are gone now ... - is that a problem ? or was it a mistake that they were there in galGal5's case ?

pkerpedjiev commented 5 years ago

It's not a huge problem if you're not using them but we should probably keep them here. The reason that script removed them from galGal6 is that the alternate contigs have different names in galGal5. They have names like chr16_NT_* whereas galGal6 has names like chr16_NW_*. Not sure why.

I usually just rearrange the main contigs by hand and leave the alternates in the order that they were in before.

pkerpedjiev commented 5 years ago

I just pushed galGal6 to master and created a new release 0.2.22 that includes galGal6. Let me know if that works for you and we can close this PR.

sergpolly commented 5 years ago

@pkerpedjiev Sounds great! thank you! I hope that solves @gibcus original question https://github.com/pkerpedjiev/negspy/issues/4#issuecomment-494041362 where he couldn't aggregate bedpe