Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds29k
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Seattle, WA USA
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http://bitsumma.com/
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AlexReynolds
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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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Comment: C: Get intersection of files occuring in at least 2 files?
... 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 Reynolds29k
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Comment: C: Get intersection of files occuring in at least 2 files?
... 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 Reynolds29k
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Comment: C: Petition to demand that the Federal German Government release all genomic data o
... 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 Reynolds29k
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Comment: C: Petition to demand that the Federal German Government release all genomic data o
... 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 Reynolds29k
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Answer: A: How to generate start & end coordinates for each chromosome of human ref genome
... 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 Reynolds29k
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Comment: C: Get intersection of files occuring in at least 2 files?
... 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 Reynolds29k
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Comment: C: featureCounts does not summarise counts from added/reporter genes
... 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 Reynolds29k
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Answer: A: Get intersection of files occuring in at least 2 files?
... 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 Reynolds29k
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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 Reynolds29k
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Comment: C: Identify TF binding motif for a given gene
... This biostars post may help: https://www.biostars.org/p/359642/#359660 ...
written 21 days ago by Alex Reynolds29k

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Commentator 11 days ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Teacher 21 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?
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Teacher 11 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 11 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?
Popular Question 12 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
Scholar 3 months ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
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Scholar 3 months ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
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Scholar 3 months ago, created an answer that has been accepted. For A: Count total base pairs in bedfile B that overlap bedfile A

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