Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds27k
Reputation:
27,300
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Trusted
Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
14 minutes ago
Joined:
9 years, 3 months ago
Email:
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

<prev • 2,373 results • page 1 of 238 • next >
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Answer: A: Can we consider Bioinformatics as a engineering discipline?
... Engineers have specific degrees and certification processes in most, but not all countries. What this legal framework entails for you will depend on where you live. Where there are regulations, engineers often accept civil and/or criminal liability when their products hurt or kill people. They put ...
written 6 days ago by Alex Reynolds27k
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Comment: C: How to report genomic intervals essentailly overlapping in all files?
... I offered a solution that generalizes to many files but ended up deleting it. Sorry and good luck! ...
written 14 days ago by Alex Reynolds27k
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Comment: C: extracting gene names
... I suggest reading the answers in the linked thread, which include explanations of what to do and how to do it. ...
written 15 days ago by Alex Reynolds27k
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Comment: C: How to make an Exon Junction BED file from ENSEMBL
... https://www.biostars.org/p/315680/#315683 ...
written 16 days ago by Alex Reynolds27k
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Comment: C: extracting gene names
... https://www.biostars.org/p/61513/ ...
written 16 days ago by Alex Reynolds27k
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Answer: A: Trascription factor binding site prediction
... Some answers I've written on searching promoters for TFBS using FIMO: https://www.biostars.org/p/359642/ https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491 Adjust for your organism, assembly, and TF databases of interest. ...
written 16 days ago by Alex Reynolds27k
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Comment: C: Extract coordinates of upstream region up to closest coding region in R
... Okay, I provided a solution that should work reasonably generically with any set of annotations, including yours. Feel free to give it a shot if you like. ...
written 19 days ago by Alex Reynolds27k
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Answer: A: Extract coordinates of upstream region up to closest coding region in R
... Perhaps the following script (with modifications specific to the genes you want to use) will help. This `bash` script combines BEDOPS `bedmap`, `bedops`, and `gtf2bed` with `awk` processing steps to conditionally process promoter regions, where there are overlaps with gene annotations. #!/bin ...
written 19 days ago by Alex Reynolds27k
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Comment: C: Extract coordinates of upstream region up to closest coding region in R
... Do you have a situation where a 2kb window upstream of a gene can overlap another 2kb window from another gene? ...
written 23 days ago by Alex Reynolds27k
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Answer: A: Extract coordinates of upstream region up to closest coding region in R
... You could use BEDOPS `closest-features` to find nearest upstream features and test if they are within range with `bedmap --range`, filtering them or scanning further upstream, depending on what you want to do next. ...
written 23 days ago by Alex Reynolds27k

Latest awards to Alex Reynolds

Teacher 2 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 4 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 10 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?
Epic Question 16 days ago, created a question with more than 10,000 views. For Converting TCGA expression data from FPKM to TPM
Scholar 5 weeks ago, created an answer that has been accepted. For A: Search dbSNP for hg19 based coordinates
Appreciated 5 weeks ago, created a post with more than 5 votes. For samtools idxstats on indexed BAM failed
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Method Of Converting Bigwig File Format Into Bed Format?
Teacher 5 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 5 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?
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Any Method Of Converting Bigwig File Format Into Bed Format?
Teacher 5 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 Cubemaker - visualize three-dimensional datasets via the web
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?
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?
Great Question 9 weeks ago, created a question with more than 5,000 views. For Where To Find Ensembl Tss Annotations?
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?
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?
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?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Find Nearest Gene Upstream Using Mysql And Perl Program
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?
Scholar 11 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 12 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 12 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

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