Moderator: Alex Reynolds
Alex Reynolds ♦ 31k
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- Seattle, WA USA
- Website:
- http://bitsumma.com/
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- AlexReynolds
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- Last seen:
- 10 hours ago
- Joined:
- 10 years, 10 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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... What UCSC visualizes in its browser uses a 1-based index, because most of us have ten digits on our hands and that makes counting of things more "natural" in a visual rendering.
What UCSC publishes as datasets are usually (not always, but generally) zero-based, half-open, which helps make distance ...
written 21 hours ago by
Alex Reynolds ♦ 31k
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... The start is actually zero; the convention is 0-based, half-open. ...
written 22 hours ago by
Alex Reynolds ♦ 31k
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... A good, generic way to do this is to get the `fetchChromSizes` tool from the [UCSC Kent utilities kit][1]:
$ fetchChromSizes hg19 | awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2; }' | sort-bed - > hg19.bed
You can use this for `hg19`, `hg38`, `mm10`, etc. Just swap out the assembly name.
...
written 22 hours ago by
Alex Reynolds ♦ 31k
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... Your question seems unclear about the exact operation being performed, and your output looks suspect (duplicate rows in the output, but the first file contains different "sites").
Can you please simplify the question and double-check what the input and output should look like? ...
written 2 days ago by
Alex Reynolds ♦ 31k
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... If you want performance, learn C. If you want data structures and OOP, learn C++. ...
written 8 days ago by
Alex Reynolds ♦ 31k
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... When using liftOver, one approach is to do liftOver in both directions, i.e., from species A to B, and then back from the liftOver result from B back to species A:
A -> B -> A'
Then use `bedmap` or similar to get those intervals from A that are also found in A'.
This gives a conservati ...
written 9 days ago by
Alex Reynolds ♦ 31k
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... Some clean-up work is needed. Export your file from Excel as a tab-delimited file. Clean it of Microsoft line endings and make a headerless, sorted file via `sort-bed`:
$ tr -d '\r' elements.tsv | sort-bed - > elements.bed
Then via `bedops`:
$ CHROM=chr1
$ START=12345
$ END=234 ...
written 16 days ago by
Alex Reynolds ♦ 31k
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... You can use the bin file directly as a BED file, using mapping operations via `bedmap` (https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html). Conversion to GTF is unnecessary. ...
written 16 days ago by
Alex Reynolds ♦ 31k
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... OmniGraffle would do most of the hard work in a few minutes: https://www.omnigroup.com/omnigraffle/ ...
written 16 days ago by
Alex Reynolds ♦ 31k
0
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... BED is generally an unbound format after the third column, with some very specific exceptions, so BED-to-GTF is not straightforward. Usually you can go the other way, however; see `gtf2bed` for an example.
That said, going from bins in a BED file to GTF doesn't really make sense. GTF is used to re ...
written 17 days ago by
Alex Reynolds ♦ 31k
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For A: No PhyloP score for first stretch of chromosome?
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For Cubemaker - visualize three-dimensional datasets via the web
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For A: Genomic coordinates for Cytogenetic bands with R
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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: No PhyloP score for first stretch of chromosome?
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For A: Genomic coordinates for Cytogenetic bands with R
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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: No PhyloP score for first stretch of chromosome?
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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 Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
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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: No PhyloP score for first stretch of chromosome?
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created an answer with at least 3 up-votes.
For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For A: Download Clustal Omega on Mac OS
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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: No PhyloP score for first stretch of chromosome?
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5 months ago,
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For A: Download Clustal Omega on Mac OS
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For A: Strategy For Dealing With Reference Files (Genomes) That Are Larger Than The Sof
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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