Moderator: Alex Reynolds

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Alex Reynolds26k
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Seattle, WA USA
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http://dropbit.com/
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AlexReynolds
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an hour ago
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8 years, 11 months ago
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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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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... I would just script it. It's just the equivalent of a `do...while` loop. taking samples that meet your criteria and ignoring the rest, until you hit some predefined limit: validSamples = [] // empty list of valid samples N = 1234 // desired number of samples // draw samples until you g ...
written 1 day ago by Alex Reynolds26k
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Comment: C: How To Randomly Sample A Subset Of Lines From A Bed File
... Rejection sampling might work. You would generate an element of desired average length, measure reads, and either keep or discard, depending of whether that measurement falls within the bounds of the read statistics for your target peak set. Keep sampling until you have as many elements as you need ...
written 2 days ago by Alex Reynolds26k
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Answer: A: Ensembl ID conversion - other than Uniprot
... Here's a way to use mygene.info to script queries. Say you have this script called `mapEnsemblGeneToUniprot.py`: #!/usr/bin/env python import sys import mygene mg = mygene.MyGeneInfo() genes = [] for line in sys.stdin: genes.append(line.strip()) ...
written 7 days ago by Alex Reynolds26k
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Answer: A: Get Rs Number Based On Chromosome and Position
... If you have disk space, you can set up a local copy of dbSNP for your assembly of interest, e.g. `hg38`: $ VCF=ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz $ wget -qO- ${VCF} | gunzip -c - | convert2bed --input=vcf --sort-tmpdi ...
written 7 days ago by Alex Reynolds26k
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Answer: A: Extending BED intervals
... With `bedops --range`: $ bedops --range 325 --everything in.bed > out.bed https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html ...
written 8 days ago by Alex Reynolds26k
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Comment: C: Target genes of position-specific transcription factors
... Sorry, try adding ticks around the `awk` condition: bedops -u <( awk '($6="+")' gencode.v29.chr_patch_hapl_scaff.annotation.bed | ... ) ...
written 8 days ago by Alex Reynolds26k
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Comment: C: Jupyter Notebook reading in data
... Post code. You can post your notebook on Github for free, for instance. ...
written 8 days ago by Alex Reynolds26k
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Comment: C: Python script for generating Genomic windows of intervals 50kbp for Human refere
... If you want bins without CNVs: $ fetchChromSizes hg19 | awk '{print $1"\t0\t"$2}' | sort-bed - | bedops --chop 50000 -x - > hg19.bins.bed $ bedmap --count --echo --delim '\t' hg19.bins.bed cnvs.bed | awk '($1 == 0)' | cut -f2- > hg19.bins.cnvLess.bed That `awk` bit can be adjusted to ...
written 9 days ago by Alex Reynolds26k
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Answer: A: How to extract the same mapped region by multiple samples ?
... Using BEDOPS `bedops --merge`, simply: $ bedops --merge <(bam2bed < A.bam) <(bam2bed < B.bam) <(bam2bed < C.bam) > answer.bed This uses three BED streams as an example, but you can merge as many BED files as you want, in case you have an arbitrary number of BAM files to co ...
written 9 days ago by Alex Reynolds26k
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Answer: A: Python script for generating Genomic windows of intervals 50kbp for Human refere
... You can use Kent tools and BEDOPS `bedops --chop` with standard Unix streams to do this quickly and efficiently: $ fetchChromSizes hg19 | awk '{print $1"\t0\t"$2}' | sort-bed - | bedops --chop 50000 - > hg19.50k.bed Note that the bounds of chromosomes will almost certainly not split evenly ...
written 10 days ago by Alex Reynolds26k

Latest awards to Alex Reynolds

Teacher 6 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 10 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
Scholar 19 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 19 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?
Good Answer 22 days ago, created an answer that was upvoted at least 5 times. For A: Sam To Bed File With Counter Column
Teacher 23 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 4 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 4 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 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?
Scholar 5 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
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Sam To Bed File With Counter Column
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: How to read fastq file with Python
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 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?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: How To Create Mutation Diagram In R Or In Any Tools?
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?
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: How To Randomly Sample A Subset Of Lines From A Bed File
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?
Scholar 7 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 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?
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?
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
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?

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