Moderator: Ryan Dale
Ryan Dale ♦ 4.7k
- Reputation:
- 4,680
- Status:
- Trusted
- Location:
- Bethesda, MD
- Website:
- https://github.com/daler
- Twitter:
- @daler_t
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 months, 2 weeks ago
- Joined:
- 7 years, 11 months ago
- Email:
- d*****@niddk.nih.gov
A benthic ecologist by training, but now a bioinformatician at NIH's National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Cellular and Developmental Biology.
Currently studying the relationship of chromatin conformation and gene regulation.
Please note: any opinions expressed here are my own and not those of my employer.
Posts by Ryan Dale
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Comment:
C: ChromHMM Output Descriptions
... The label of each state is subjective. Coming up with good labels requires looking carefully at the enrichments (from running OverlapEnrichment) and emissions heatmaps to decide what you want to name them. ...
written 10 months ago by
Ryan Dale ♦ 4.7k
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... Sounds like you're running on a headless server with no X11 windows. In that case add these two lines to the very beginning:
import matplotilb
matplotlib.use('agg')
see http://stackoverflow.com/questions/2801882/generating-a-png-with-matplotlib-when-display-is-undefined for more details an ...
written 14 months ago by
Ryan Dale ♦ 4.7k
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... If you have enough RAM and are OK with Python:
import pybedtools
from matplotlib import pyplot as plt
sizes = [len(i) for i in pybedtools.BedTool('my.bed')]
plt.hist(sizes)
plt.savefig('hist.png')
plt.show()
...
written 14 months ago by
Ryan Dale ♦ 4.7k
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... The `gffutils` python package can help with this: https://daler.github.io/gffutils
It will infer the gene and transcript extents; doing so is the default behavior for GTF files. The following will import the GTF into a sqlite3 database (which you can use for other things if needed) and then output ...
written 14 months ago by
Ryan Dale ♦ 4.7k
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... As you mention, ChromHMM expects read counts. Even if you transform your data somehow to make it work with ChromHMM, how will you interpret the results? I would expect the HMM to see the imputed data as a combination of the other vars anyway, making it redundant. I guess I'm not sure there's an adva ...
written 14 months ago by
Ryan Dale ♦ 4.7k
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... FYI, versions 0.4.4 thru 0.7.0 are available for Linux & OSX via [bioconda][1]
[1]: https://bioconda.github.io ...
written 16 months ago by
Ryan Dale ♦ 4.7k
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... We have an opening for a post-baccalaureate bioinformatics trainee in the Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health in Bethesda, MD. This is a one year appointment, starting as soon as May 2 ...
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Answer:
A: ChIP-seq vs. RNA-seq
... Map them both to a reference; the RNA-seq library will be more likely to have splice junctions (look for "N" in the BAM cigar string) and will be sparse in intergenic regions, while the ChIP-seq will have more even coverage, less dynamic range, and will probably have some low-level signal in most pl ...
written 18 months ago by
Ryan Dale ♦ 4.7k
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... Fidel, this is amazing. A much-needed and much-appreciated initiative. ...
written 18 months ago by
Ryan Dale ♦ 4.7k
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1.9k
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... Are you using a Clontech kit by any chance? ...
written 20 months ago by
Ryan Dale ♦ 4.7k
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For A: How To Plot/Visualise Tfbs Positions Relative To Tss For Thousands Of Genes?
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For A: Making gene annotation from a GTF file
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