Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds25k
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25,210
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Location:
Seattle, WA USA
Website:
http://dropbit.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
6 hours ago
Joined:
8 years, 9 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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Comment: C: Illegal Division by zero
... Debug the values of the array at different stages of the script. Check that the array is initialized to non-zero values, or that a pseudocount is applied correctly. ...
written 2 days ago by Alex Reynolds25k
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Answer: A: Get gene names from ensembl ID or gene region
... You could use Python `mygene` with the `ensembl.transcript` scope: #!/usr/bin/env python import sys import mygene mg = mygene.MyGeneInfo() names = [] for line in sys.stdin: names.append(line.rstrip()) for name in names: result = mg.que ...
written 7 days ago by Alex Reynolds25k
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Comment: C: Determine peak summits after IDR analysis
... If `A.bed` is your narrowPeak file: $ awk -vOFS="\t" -vFS="\t" '{ print $1, $2, $3, $4"%%"$10 }' A.bed > A.custom.bed The ID of `A.custom.bed` contains the original peak ID, concatenated with the summit position, using `%%` as a delimiter. Repeat for peak files `B.bed` and `C.bed`. Once y ...
written 7 days ago by Alex Reynolds25k
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Comment: C: Efficiently performing intersections for multiple subsets of a BED file
... Okay, your input is a little different than I assumed. Perhaps try a regular expression, instead: $ for gene in `cat genes.txt`; do bedops --intersect A.bed <(awk -vgene=${gene} -vOFS="\t" -vFS="\t" '{ regex = "^"gene; if ($4 ~ regex) { print $0; } }' B.bed) | awk -vgene=${gene} -vOFS="\t" ...
written 8 days ago by Alex Reynolds25k
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Comment: C: Efficiently performing intersections for multiple subsets of a BED file
... Can you do the same for `A.bed` and `B.bed`: $ cat -te A.bed | head ... $ cat -te B.bed | head ... I'm reviewing things and I'm not sure what's wrong. ...
written 8 days ago by Alex Reynolds25k
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Comment: C: Efficiently performing intersections for multiple subsets of a BED file
... What happens if you run: $ for gene in `cat genes.txt`; do echo ${gene}; done Also, do you have any weird line endings in `genes.txt`? Perhaps copy and paste the output from running this so we can take a look: $ cat -te genes.txt | head ...
written 8 days ago by Alex Reynolds25k
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Comment: C: Efficiently performing intersections for multiple subsets of a BED file
... Are you using the built-in `awk` on OS X? If so, you might use Homebrew to install GNU awk: `brew install awk`. ...
written 8 days ago by Alex Reynolds25k
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Answer: A: Determine peak summits after IDR analysis
... Use `awk` to grab the summit column from a peak file and put it into the ID field (fifth column): $ awk '{ print ... }' A > A.custom Repeat for inputs B and C. Map the merged custom intervals to the customized intervals, to get the IDs contained with the merged interval: $ bedmap --ec ...
written 8 days ago by Alex Reynolds25k
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Comment: C: How to color subset of row ?
... Hello Björn! We believe that this post does not fit the main topic of this site. This is not a bioinformatics question. You might ask on Stack Overflow. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you ...
written 8 days ago by Alex Reynolds25k
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Answer: A: How do i extract rows from a bedfile that have a certain bedscore?
... Assuming five-column BED, with the score or signal in the fifth column: $ awk '$5>100' in.bed > out.bed If you're working with a bedGraph file: $ awk '$4>100' in.bedGraph > out.bedGraph ...
written 9 days ago by Alex Reynolds25k

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 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?
Great Question 4 days ago, created a question with more than 5,000 views. For Getting list of chromosome names from indexed BAM file
Teacher 9 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 9 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?
Appreciated 9 days ago, created a post with more than 5 votes. For samtools idxstats on indexed BAM failed
Teacher 9 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 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?
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
Commentator 16 days ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
Appreciated 18 days ago, created a post with more than 5 votes. For A: How to read fastq file with Python
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
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 21 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 21 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 22 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 22 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 24 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 27 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 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?

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