Moderator: Alex Reynolds

gravatar for Alex Reynolds
Alex Reynolds27k
Reputation:
26,660
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Location:
Seattle, WA USA
Website:
http://bitsumma.com/
Twitter:
AlexReynolds
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Google Scholar Page
Last seen:
10 hours ago
Joined:
9 years 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: Historical list of of Affymetrix arrays
... The annotation files for [HT_HG-U133A][1] and [HG-U133 Plus 2.0][2] are different. Those annotation files might be useful for mapping probe IDs to gene IDs. You might investigate those annotations more closely to see where there are differences for probes of interest. I did not check the other ar ...
written 22 hours ago by Alex Reynolds27k
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Answer: A: R RGL plot3d different symbols
... Perhaps this example may help: point.styles <- sample(10:19, 10, replace=T) x1 <- sort(rnorm(10)) y1 <- rnorm(10) z1 <- rnorm(10) + atan2(x1, y1) x2 <- sort(rnorm(10)) y2 <- rnorm(10) z2 <- rnorm(10) + atan2(x2, y2) x3 <- sort(rnorm(10)) y ...
written 3 days ago by Alex Reynolds27k
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Comment: C: Looking for a database containing the least-conserved, most highly polymorphic S
... There are answers on biostars to deal with parts 1 and 2. Should be easy to find with a little searching. ...
written 6 days ago by Alex Reynolds27k
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Answer: A: Looking for a database containing the least-conserved, most highly polymorphic S
... 1. Download dbSNP and convert from VCF to BED with BEDOPS `vcf2bed`. $ vcf2bed < (gunzip -c dbSNP.vcf.gz) > dbSNP.bed 2. Download phyloP44 or other alignments and convert from WIG to BED with BEDOPS `wig2bed`. $ wig2bed < (gunzip -c phyloP.wig.gz) > phyloP.bed Fil ...
written 6 days ago by Alex Reynolds27k
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Answer: A: Need to systematically identify genes within some distance of a response element
... Via BEDOPS `bedmap`: $ bedmap --range 100000 --echo --echo-map response-elements.bed genes.bed > answer.bed If you don't have genes in BED format, but in GFF format, that's easy to fix: $ bedmap --range 100000 --echo --echo-map response-elements.bed <(gff2bed < genes.gff) > ...
written 8 days ago by Alex Reynolds27k
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Comment: C: How to merge overlapping ranges by R/Python?
... Try BEDOPS, maybe, with the example given. If you need to, use `awk` to reorder columns into a minimally three-column file, where the first three columns are: chromosome, start, and stop position. ...
written 18 days ago by Alex Reynolds27k
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Answer: A: How to merge overlapping ranges by R/Python?
... You could use `bedops --merge` to merge intervals in a sorted BED file: $ bedops --merge in.bed > out.bed A BED file is just a tab-delimited text file, minimally three columns, which specify chromosome, start, and stop attributes of each interval, respectively. You can export such a file fr ...
written 18 days ago by Alex Reynolds27k
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Answer: A: Generate a bar plot in R
... Starting with a data frame called `d`. Make a column called `gene` that assigns each row/gene to a gene name `GSM1234`, etc. Make a column called `treatment`, which is a categorical factor that assigns each row's gene to `normal` or `cancer`. Make a column called `expression`, which contains the ...
written 21 days ago by Alex Reynolds27k
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Answer: A: Why finding genes in a genomic DNA sequence is difficult?
... There is more to a gene than what codes for a protein (or codes for the transcript that gets turned into a protein, which is where the start/stop codons partially come in). Promoters, enhancers, intron-exon junctions, other regulatory regions, etc. are all parts of a gene that change how transcrip ...
written 27 days ago by Alex Reynolds27k
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Answer: A: BEDOPS bedmap tool usage
... In the case of your two snippets, `NAN`s will be returned because there are no overlaps between elements in the reference and map sets. More generally, however, the `--mean` operator is simply applied on the score data in map elements, without consideration for the length of the overlapping element ...
written 27 days ago by Alex Reynolds27k

Latest awards to Alex Reynolds

Teacher 3 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 7 days ago, created a post with more than 5 votes. For A: Find Nearest Gene Upstream Using Mysql And Perl Program
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Scholar 17 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
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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
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