Moderator: Alex Reynolds
Alex Reynolds ♦ 27k
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- Seattle, WA USA
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- http://bitsumma.com/
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- Joined:
- 9 years 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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... 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 Reynolds ♦ 27k
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... 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 Reynolds ♦ 27k
1
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... 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 Reynolds ♦ 27k
3
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... 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 Reynolds ♦ 27k
2
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... 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 Reynolds ♦ 27k
0
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170
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... 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 Reynolds ♦ 27k
3
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... 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 Reynolds ♦ 27k
3
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1
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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 Reynolds ♦ 27k
3
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1
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180
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... 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 Reynolds ♦ 27k
3
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1
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156
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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 Reynolds ♦ 27k
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