Moderator: Alex Reynolds
Alex Reynolds ♦ 27k
- Reputation:
- 27,300
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- Location:
- Seattle, WA USA
- Website:
- http://bitsumma.com/
- Twitter:
- AlexReynolds
- Scholar ID:
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- Last seen:
- 14 minutes ago
- Joined:
- 9 years, 3 months ago
- Email:
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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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... 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 Reynolds ♦ 27k
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... I offered a solution that generalizes to many files but ended up deleting it. Sorry and good luck! ...
written 14 days ago by
Alex Reynolds ♦ 27k
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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 Reynolds ♦ 27k
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... https://www.biostars.org/p/315680/#315683 ...
written 16 days ago by
Alex Reynolds ♦ 27k
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Comment:
C: extracting gene names
... https://www.biostars.org/p/61513/ ...
written 16 days ago by
Alex Reynolds ♦ 27k
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... 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 Reynolds ♦ 27k
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... 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 Reynolds ♦ 27k
0
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... 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 Reynolds ♦ 27k
0
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2
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115
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... 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 Reynolds ♦ 27k
0
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... 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 Reynolds ♦ 27k
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For Converting TCGA expression data from FPKM to TPM
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For A: Search dbSNP for hg19 based coordinates
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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: Do these warning messages during my bedops install mean bedops won't work proper
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