Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds17k
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Location:
Seattle, WA USA
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http://dropbit.com/
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AlexReynolds
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Last seen:
23 minutes ago
Joined:
7 years, 3 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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Answer: A: How to append a data.frame in R with new data
... You could have a function called `fetch_id()` that returns a record for a given `id`: fetch_id <- function(id) { return(efetch(id, db=db, rettype = 'gp', retmode = retmode, retmax = returnAmount)); } Then, given a vector of IDs: ids <- c(124511, 124512, 124513, ... ) you can pre-al ...
written 1 day ago by Alex Reynolds17k
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Comment: C: How to append a data.frame in R with new data
... Probably not a good idea to name a variable after a keyword (`list`). ...
written 1 day ago by Alex Reynolds17k
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Answer: A: error with number of fields in bedtools
... You could try `bedops`: $ bedops --not-element-of -1 B.bed A.bed > answer.bed ...
written 1 day ago by Alex Reynolds17k
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Answer: A: How to create a new bigwig file defined by a subset of bed file?
... Convert from bigwig to wiggle: $ bigWigToWig data.bw data.wig Convert from wiggle to bed: $ wig2bed < data.wig > data.bed Filter the bed file based on your peak subset, and make a bedgraph file from the subset: $ sort-bed peak_subset.unsorted.bed > peak_subset.bed $ bed ...
written 4 days ago by Alex Reynolds17k
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Answer: A: Make a sequence logo from information in a file?
... 1. Export your 15 positions to a [UCSC BED][1]-formatted text file 2. Use a script like [bed2faidxsta][2] to convert the BED file to a FASTA-formatted file 3. Use a program like [Weblogo][3] to convert the FASTA file to a sequence logo image file or PWM [1]: https://genome.ucsc.edu/FAQ/FAQformat ...
written 8 days ago by Alex Reynolds17k
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Answer: A: from txt to bed
... Using `sed` is problematic because it isn't portable between GNU and BSD versions. You might use `awk` instead: $ awk -F"[:-]" 'BEGIN{ OFS="\t"; }{ print $1, $2, $3; }' in.txt > out.bed For example: $ echo chrx:11111-2222 | awk -F"[:-]" 'BEGIN{ OFS="\t"; }{ print $1, $2, $3; }' chr ...
written 8 days ago by Alex Reynolds17k
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Answer: A: How to cluster reads within the fastq file? Is their any tool?
... You can use R to do supervised hierarchical clustering of sequence strings, using edit or [Levenshtein distance][1] as your distance metric. SO: [Text clustering with Levenshtein distances][2] With some R chops, you should be able to annotate the tree leaf labels (sequences) with the read IDs they ...
written 8 days ago by Alex Reynolds17k
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Answer: A: Figure quality browser tracks
... I wrote a tool called [soda.py][1] that automates making browsable web galleries from PDF-formatted UCSC browser snapshots. Set up your browser session with your BW files and other tracks (conservation, etc.). Grab the session ID(§) and feed that and your BED file of intervals-of-interest to *soda ...
written 8 days ago by Alex Reynolds17k
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Answer: A: Retrieving gene details
... You could use UCSC Goldenpath; e.g. for `hg19`: $ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/knownGene.txt.gz | gunzip -c > knownGene.txt You could use the `kgXref` table to map naming schemes via `grep` etc.: $ wget -qO- http://hgdownload.cse.ucsc.edu/goldenpath ...
written 12 days ago by Alex Reynolds17k
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Answer: A: how to rotate chordDiagram in library circlize?
... Perhaps set `start.degree` in `circos.par`: > library(circlize) > circos.par(start.degree = 123) > circos.initialize(...) ... Or print out a PDF or SVG and rotate it in Adobe Illustrator. ...
written 12 days ago by Alex Reynolds17k

Latest awards to Alex Reynolds

Teacher 1 day 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 14 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?
Teacher 14 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?
Teacher 15 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?
Scholar 15 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher 16 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?
Scholar 19 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher 20 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?
Teacher 20 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?
Scholar 20 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Appreciated 20 days ago, created a post with more than 5 votes. For A: How To Randomly Sample A Subset Of Lines From A Bed File
Teacher 20 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?
Teacher 26 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?
Scholar 26 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher 26 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?
Scholar 28 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar 28 days ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar 4 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar 4 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Scholar 6 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher 6 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?
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: How To Randomly Sample A Subset Of Lines From A Bed File
Scholar 6 weeks ago, created an answer that has been accepted. For A: Do these warning messages during my bedops install mean bedops won't work proper
Teacher 6 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?

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