Comments (8)
Did you want to have hard coded BAM and vcfTabix examples in the repository?
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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.
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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.
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That looks good -- I'll grab small parts of those files to use.
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Sounds good. I am looking into making a vcfTabix file, but haven't found a could method, have you?
from trackhub.
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.
from trackhub.
That might be the best way to go. I will see if I can find a VCF file.
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This is now implemented with @evajason's work with all the example hubs, using data from UCSC.
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Related Issues (20)
- Add support for superTracks HOT 1
- how to setup and run HOT 1
- assembly hub support HOT 1
- symlink to staging area before uploading HOT 1
- `pip install` error HOT 4
- priority must be float not integer HOT 2
- ViewTrack url not mapped to bigDataUrl HOT 2
- Track parent on/off HOT 2
- ImportError: cannot import name Hub HOT 7
- bigWig file names HOT 3
- ssh_askpass error HOT 1
- Are there some features of trackDB that are not supported on trackhub?
- test scripts HOT 1
- Inconsistent method names for adding tracks HOT 3
- support for multiWig tracks
- Broken link in Quickstart docs
- example hubs don't go to a good location
- Support URL for 2bit files
- parse UCSC's settings HOT 6
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