example data

[daler]

currently have bigBed and bigWig example data, but need to make some BAM and vcfTabix example data as well

[vsmalladi]

Did you want to have hard coded BAM and vcfTabix examples in the repository?

[daler]

Yep. This is what I do with pybedtools, and it works out pretty well. It's really useful for testing and replicating the exact results on other machines.

They need to be small though so the repo and distribution don't get to big (<<1MB). Do you have any good examples on hand? Or I can just make some random ones similar to the example bigWigs.

[vsmalladi]

I have some whole genome example files in https://github.com/ENCODE-DCC/trackhub_example, however this are quite big. You could choose data from 1 chromosome to make sure the distribution is <<1MB.

[daler]

That looks good -- I'll grab small parts of those files to use.

[vsmalladi]

Sounds good. I am looking into making a vcfTabix file, but haven't found a could method, have you?

[daler]

I don't use VCF in my work, so it's the least familiar format to me. I don't know of any method for generating random VCF. BEDTools/pybedtools handles the format, so it should be able to randomize an existing VCF easily enough.

[vsmalladi]

That might be the best way to go. I will see if I can find a VCF file.

[daler]

This is now implemented with @evajason's work with all the example hubs, using data from UCSC.