Moderator: Brad Chapman
Brad Chapman ♦ 9.1k
- Reputation:
- 9,090
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- Trusted
- Location:
- Boston, MA
- Website:
- http://bcbio.wordpress...
- Twitter:
- chapmanb
- Last seen:
- 4 months, 3 weeks ago
- Joined:
- 7 years, 5 months ago
- Email:
- c*******@50mail.com
Biologist and programmer at Harvard School of Public Health
Posts by Brad Chapman
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... Thanks for this pointer. As an additional data point, I ran into a similar issue in a restricted build environment for bioconda and adding perl to the environment fixes it for me. ...
written 7 months ago by
Brad Chapman ♦ 9.1k
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... For processing with sra you'll want to convert into standard fastq format using the SRA toolkit (http://www.ncbi.nlm.nih.gov/books/NBK158900/). In bcbio, you can add a custom reference genome for tuberculosis (https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#adding-custom- ...
written 20 months ago by
Brad Chapman ♦ 9.1k
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... It's possible to include it, but it would need integration work to include it as a new aligner. Documentation on writing that code is here:
https://bcbio-nextgen.readthedocs.org/en/latest/contents/code.html#aligner
Out of curiousity, why do you prefer BBMap over other integrated aligners in bcbio ...
written 20 months ago by
Brad Chapman ♦ 9.1k
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... Steve is right that the Genome in a Bottle group is still working on a native 38 build of the reference. In the short term, we've been doing work on providing a Remapped/Crossmapped version that converts the 37 reference to 38 coordinates. This isn't finished as I'm not happy with the Remapping of S ...
written 2.0 years ago by
Brad Chapman ♦ 9.1k
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Answer:
A: Tumor clonality algorithms
... We've been working on integrating clonality and heterogeneity estimation tools into bcbio (https://github.com/chapmanb/bcbio-nextgen). It's still a work in progress but we've been evaluating against internal datasets where we have external predictions of normal contamination. We've had the most succ ...
written 2.2 years ago by
Brad Chapman ♦ 9.1k
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... Shane;
Welcome to bioinformatics work. It would be easier to offer suggestions with an idea of your programming background and biological interests. As a starting point, the ADAM project has a nice contributing guide, great group of folks, and the issue tracker has 'Pick Me Up!' issues which are me ...
written 2.5 years ago by
Brad Chapman ♦ 9.1k
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... Pierre;
The source code is here:
https://github.com/konradjk/exac_browser
It looks like a MongoDB database and Python Flask webserver. It also builds on xBrowse:
https://github.com/xbrowse/xbrowse
...
written 2.5 years ago by
Brad Chapman ♦ 9.1k
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... The approach isn't species specific. The general idea is to find regions where we can reliably break analysis steps into chunks that are smaller than whole chromosomes and as balanced as possible. We do this in bcbio and it has been used across a wide variety of species without issues.
Another tool ...
written 2.6 years ago by
Brad Chapman ♦ 9.1k
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... This is absolutely possible, and as Devon mentioned similar to approaches we use in bcbio (https://github.com/chapmanb/bcbio-nextgen). In bcbio we haven't yet worked on single sample optimization. Practically we don't have users with a large number of idle cores and the use case of pushing through a ...
written 2.6 years ago by
Brad Chapman ♦ 9.1k
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... You need to have the `wigToBigWig` executable available in your PATH. The script header has a bit more documentation: https://github.com/chapmanb/bcbb/blob/796cc2a1179df6f5030212fd5e7f36540351abdb/nextgen/scripts/bam_to_wiggle.py#L23 Hope this helps get it running.
...
written 2.9 years ago by
Brad Chapman ♦ 9.1k
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