Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds29k
Reputation:
29,140
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Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
9 hours ago
Joined:
10 years, 2 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

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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 Reynolds29k
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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 Reynolds29k
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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 Reynolds29k
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Comment: C: How convert files .psl to files .bed?
... GFF and BED are two different formats. ...
written 9 days ago by Alex Reynolds29k
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Comment: C: multiple bed - merge regions IF overlapping more than xx percent of size
... I'm trying to understand the problem. Can you give me a test input that fails? Thanks! ...
written 9 days ago by Alex Reynolds29k
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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 Reynolds29k
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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 Reynolds29k
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Answer: C: Converting peak ID to gene symbol
... 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 Reynolds29k
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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 Reynolds29k
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Comment: C: How to extend variable length intervals to the same final length?
... 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 Reynolds29k

Latest awards to Alex Reynolds

Teacher 13 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: No PhyloP score for first stretch of chromosome?
Appreciated 16 days ago, created a post with more than 5 votes. For samtools idxstats on indexed BAM failed
Scholar 4 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Scholar 4 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
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?
Popular Question 5 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
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?
Popular Question 6 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 7 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Teacher 7 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 8 weeks ago, created an answer that was upvoted at least 5 times. For A: What'S Easy Framework For Writing Gui Tools In Bioinformatics
Scholar 8 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 9 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 9 weeks ago, created an answer that has been accepted. For A: Naming of FastA sequences
Scholar 9 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
Scholar 9 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 9 weeks ago, created an answer that has been accepted. For A: Count total base pairs in bedfile B that overlap bedfile A
Scholar 11 weeks ago, created an answer that has been accepted. For A: No PhyloP score for first stretch of chromosome?
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: 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
Student 12 weeks ago, asked a question with at least 3 up-votes. For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster

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