Moderator: Alex Reynolds
Alex Reynolds ♦ 29k
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- Seattle, WA USA
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- http://bitsumma.com/
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- Joined:
- 10 years, 3 months ago
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One of the developers behind the fast BEDOPS suite, whose pug Zac is the bestest pug in the world.
Posts by Alex Reynolds
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... Can you post the command you're running and perhaps provide access to your input files (or a small sample snippet)? I can run that locally and help answer your question with more specifics. ...
written 7 days ago by
Alex Reynolds ♦ 29k
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... The `bedops` tool allows more than two files (A, B, C, etc.).
Conversely, the `bedmap` tool only takes two files as arguments (reference and map).
However, if you're using `bedmap`, you can use a trick called a "process substitution" to replace the `reference.bed` or `map.bed` files.
A process ...
written 7 days ago by
Alex Reynolds ♦ 29k
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... I understand — even so, GISAID is headquartered in Germany and so would presumably be bound to German and European regulations regarding privacy, which may (or may not) apply to genomic data. Some light would be useful here. ...
written 12 days ago by
Alex Reynolds ♦ 29k
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... I agree with you in principle. I'm curious if there are GDPR regulations that constrain what GISAID and other research groups may be allowed to do regarding the (re-)distribution of genomic datasets from Europe. Or is this policy directly from GISAID, itself? I'm not a lawyer, but I wonder if there ...
written 12 days ago by
Alex Reynolds ♦ 29k
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... Instead of using R, I suggest using the [UCSC Kent Utilities][1] kit. It includes a binary called `fetchChromSizes` that is perfect for this task. The link will take you to folders you can pick from for your platform (Linux or OS X) containing pre-compiled binaries, so it is a quick download.
You ...
written 12 days ago by
Alex Reynolds ♦ 29k
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... What I mean is the case where any two regions within a single BED file overlap.
For instance, sequencing reads converted from BAM or SAM to BED will almost certainly overlap within the same file, because reads typically pile up that way.
Other types of annotations could also be problematic, in t ...
written 15 days ago by
Alex Reynolds ♦ 29k
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... It may help to run GTF files through validators. Not all GTF files are created correctly, it seems: https://www.biostars.org/p/206342/#206350 ...
written 15 days ago by
Alex Reynolds ♦ 29k
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... Here is a general approach with [BEDOPS `bedmap --count`][1], which generalizes to *N* internally-disjoint (and `sort-bed`-sorted) input files:
$ bedops --everything 1.bed 2.bed 3.bed ... N.bed \
| bedmap --count --echo --delim '\t' - \
| uniq \
| awk -v OVERLAPS=2 '$1 & ...
written 15 days ago by
Alex Reynolds ♦ 29k
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Comment:
C: TFBS enrichiment analysis
... Some possible answers:
1. In the approach I describe, FIMO scans the entire genome for binding sites (in practice, minus masked regions) — more than just promoters. So using `bedmap` restricts the set of binding sites to those which overlap by at least (in this case) three bases with a promoter re ...
written 20 days ago by
Alex Reynolds ♦ 29k
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... This biostars post may help: https://www.biostars.org/p/359642/#359660 ...
written 21 days ago by
Alex Reynolds ♦ 29k
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For A: Do these warning messages during my bedops install mean bedops won't work proper
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For A: Count total base pairs in bedfile B that overlap bedfile A
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