Moderator: Alex Reynolds
Alex Reynolds ♦ 26k
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- Seattle, WA USA
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- Joined:
- 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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... 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 Reynolds ♦ 26k
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5
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... 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 Reynolds ♦ 26k
1
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... 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 Reynolds ♦ 26k
4
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... 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 Reynolds ♦ 26k
2
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2
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88
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2
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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 Reynolds ♦ 26k
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... 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 Reynolds ♦ 26k
0
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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 Reynolds ♦ 26k
1
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3
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172
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... 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 Reynolds ♦ 26k
1
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2
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... 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 Reynolds ♦ 26k
2
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3
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172
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3
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... 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 Reynolds ♦ 26k
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