Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds31k
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Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Last seen:
10 hours ago
Joined:
10 years, 10 months ago
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a************@gmail.com

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: genome coordinates hg19 from UCSC genome browser
... 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 Reynolds31k
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Comment: C: genome coordinates hg19 from UCSC genome browser
... The start is actually zero; the convention is 0-based, half-open. ...
written 22 hours ago by Alex Reynolds31k
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Answer: A: genome coordinates hg19 from UCSC genome browser
... 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 Reynolds31k
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Comment: C: Making disjoint chromosomal sites contiguous with awk
... 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 Reynolds31k
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Answer: A: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
... If you want performance, learn C. If you want data structures and OOP, learn C++. ...
written 8 days ago by Alex Reynolds31k
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Comment: C: How to keep the input bed coordinates of a bed?
... 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 Reynolds31k
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Answer: A: retrieving rows from a bed file
... 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 Reynolds31k
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Comment: C: How to bin a genome to different regions
... 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 Reynolds31k
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Comment: C: How to a make schematic picture for RNA-seq steps
... OmniGraffle would do most of the hard work in a few minutes: https://www.omnigroup.com/omnigraffle/ ...
written 16 days ago by Alex Reynolds31k
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Comment: C: How to bin a genome to different regions
... 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 Reynolds31k

Latest awards to Alex Reynolds

Scholar 6 days ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 8 days ago, 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?
Appreciated 26 days ago, created a post with more than 5 votes. For Cubemaker - visualize three-dimensional datasets via the web
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Genomic coordinates for Cytogenetic bands with R
Teacher 8 weeks ago, 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?
Teacher 8 weeks ago, 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?
Scholar 8 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Good Answer 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Genomic coordinates for Cytogenetic bands with R
Teacher 9 weeks ago, 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?
Scholar 9 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 10 weeks ago, 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?
Scholar 10 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Student 3 months ago, asked a question with at least 3 up-votes. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Teacher 3 months ago, 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?
Scholar 3 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 3 months ago, 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?
Teacher 4 months ago, 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?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Download Clustal Omega on Mac OS
Teacher 4 months ago, 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?
Great Question 4 months ago, created a question with more than 5,000 views. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
Scholar 4 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Download Clustal Omega on Mac OS
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Strategy For Dealing With Reference Files (Genomes) That Are Larger Than The Sof
Teacher 5 months ago, 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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