Moderator: Alex Reynolds
Alex Reynolds ♦ 19k
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- Joined:
- 7 years, 6 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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Comment:
C: tabix for ID column
... Don't overthink it. [Link `gzip` and `gunzip` to `pigz`][1]. Then:
$ gzip -c snps.vcf > snps.gz
$ zgrep rs1234 snps.gz > answer.txt
A database is way overkill.
[1]: https://unix.stackexchange.com/a/87120/38132 ...
written 1 day ago by
Alex Reynolds ♦ 19k
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... There are [lots of answers][1] on this question already on Biostars. Search for "[closest-features][2]" and look at the `--closest` and `--dist` options.
[1]: https://www.biostars.org/p/53587/
[2]: http://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html ...
written 8 days ago by
Alex Reynolds ♦ 19k
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... Here is an efficient solution with [BEDOPS][1], which avoids approaches with other tools that require M^N pairwise comparisons, for M elements and N sets.
Say you have N files (your specific example uses 8 files, but this shows a generic solution for N files). You want all elements from N files, wh ...
written 11 days ago by
Alex Reynolds ♦ 19k
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Comment:
C: How To Sort Bed Format File
... Yep, see: https://www.biostars.org/p/64687/#64701 ...
written 11 days ago by
Alex Reynolds ♦ 19k
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... It looks like a pretty straightforward scripting problem. You could efficiently solve overlaps at the end with `bedops --partition`, which is not available in other toolkits, as far as I know.
Here's a script you can use to subsample from a shuffled list of intervals:
#!/usr/bin/env python
...
written 13 days ago by
Alex Reynolds ♦ 19k
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... I'm just explaining one way to do things, if your inputs can be set up correctly. You may need to convert files to sorted BED with `bigWigToWig`, `wig2bed`, `jq`, `sort-bed` etc. to do set operations. ...
written 15 days ago by
Alex Reynolds ♦ 19k
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... Merge the per-base signal (scores):
$ bedops --merge per-base-signal.bed > merged-pbs.bed
Invert the merged regions to get the "mirror" image. This "mirror" is the set of gaps in between merged stretches of signal.
Assuming `hg38`, say:
$ fetchChromSizes hg38 | awk '{ print $1"\t0\t" ...
written 15 days ago by
Alex Reynolds ♦ 19k
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... Another option is to use `bedops --chop` to make the 10k windows, instead of `awk`:
$ bedops --chop 10000 mm10.extents.bed > mm10.disjointWindows.bed
This option was added after I wrote the initial answer. ...
written 17 days ago by
Alex Reynolds ♦ 19k
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... Ah, sorry, I misread. I'm not sure why you get an empty result. I'd break things down and use `head` to see what comes out at various stages. ...
written 17 days ago by
Alex Reynolds ♦ 19k
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... Yeah, not sure why that is. Maybe do:
$ fetchChromSizes mm10 | head
and see what you get. ...
written 17 days ago by
Alex Reynolds ♦ 19k
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