Moderator: Alex Reynolds
Alex Reynolds ♦ 29k
- Reputation:
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- Location:
- Seattle, WA USA
- Website:
- http://bitsumma.com/
- Twitter:
- AlexReynolds
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- Last seen:
- 9 hours ago
- Joined:
- 10 years, 2 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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Answer:
A: public file storage
... Amazon has a 12-month free tier for S3 data storage, which allows up to 5 GB and 20k requests (https://aws.amazon.com/free/?all-free-tier.sort-by=item.additionalFields.SortRank&all-free-tier.sort-order=asc). Files can be made available to the public, with the caveat that those limits could be hi ...
written 5 days ago by
Alex Reynolds ♦ 29k
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Answer:
A: Sequences alignment program
... Depending on the length of what you're querying, there may be other tools worth considering for shorter sequence queries, in addition to `blat` (especially if working with sequences less than 20nt long).
BLAST's `blastn` has a `blastn-short` argument that may be useful here. Bowtie is another opti ...
written 6 days ago by
Alex Reynolds ♦ 29k
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Comment:
C: Sequences alignment program
... Some alignment tools do better than others, depending on sequence length and content. Can you describe a little more about the characteristics of what you're querying? That might help give you a more specific recommendation. ...
written 6 days ago by
Alex Reynolds ♦ 29k
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... GFF and BED are two different formats. ...
written 9 days ago by
Alex Reynolds ♦ 29k
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... I'm trying to understand the problem. Can you give me a test input that fails? Thanks! ...
written 9 days ago by
Alex Reynolds ♦ 29k
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Comment:
C: Converting peak ID to gene symbol
... Thanks for following up — this may help other people who have similar questions down the road. ...
written 14 days ago by
Alex Reynolds ♦ 29k
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Comment:
C: Converting peak ID to gene symbol
... I should warn that proteomics is not my field, but the format of those peak IDs gets no hits on either of the two search engines I use, so contacting the authors will probably be the best way to get an answer. Good luck! ...
written 15 days ago by
Alex Reynolds ♦ 29k
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... The paper suggests a tool called "ClinProt Tools" may have been used for peak calling, but what I could find online about this tool doesn't include much detail about the format they use for peak IDs. I would suggest getting in touch with the paper's authors and ask them for more comprehensive detail ...
written 15 days ago by
Alex Reynolds ♦ 29k
1
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Comment:
C: Converting peak ID to gene symbol
... It would be helpful to describe your data in more detail. Knowing what format of data you're using may help with recommending the right conversion and querying tools. ...
written 15 days ago by
Alex Reynolds ♦ 29k
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... Dividing `diff` by 2 when it is an odd number, probably. The `int()` function chops off the fractional part.
Sounds like this is not a problem for the original question, but might be an issue for you? This is tough because genomic intervals aren't usually fractional, so a decision would have to be ...
written 5 weeks ago by
Alex Reynolds ♦ 29k
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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15 days ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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15 days ago,
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For A: No PhyloP score for first stretch of chromosome?
Appreciated
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For samtools idxstats on indexed BAM failed
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For A: No PhyloP score for first stretch of chromosome?
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For A: No PhyloP score for first stretch of chromosome?
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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 Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
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5 weeks ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher
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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 Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
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For A: No PhyloP score for first stretch of chromosome?
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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: What'S Easy Framework For Writing Gui Tools In Bioinformatics
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For A: Do these warning messages during my bedops install mean bedops won't work proper
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For A: Do these warning messages during my bedops install mean bedops won't work proper
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9 weeks ago,
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For A: No PhyloP score for first stretch of chromosome?
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9 weeks ago,
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For A: Do these warning messages during my bedops install mean bedops won't work proper
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For A: Count total base pairs in bedfile B that overlap bedfile A
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11 weeks ago,
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For A: No PhyloP score for first stretch of chromosome?
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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
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
Scholar
11 weeks 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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12 weeks ago,
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For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
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