Moderator: Alex Reynolds
Alex Reynolds ♦ 31k
- Reputation:
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- Location:
- Seattle, WA USA
- Website:
- http://bitsumma.com/
- Twitter:
- AlexReynolds
- Scholar ID:
- Google Scholar Page
- Last seen:
- 9 hours ago
- Joined:
- 11 years, 1 month 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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... You could try splitting the BED file by chromosome:
$ sort-bed INPUT.bed > INPUT.sorted.bed
$ for CHR in `bedextract --list-chr INPUT.sorted.bed`; do bedextract ${CHR} INPUT.sorted.bed > INPUT.sorted.${CHR}.bed; done
Then run your `bigWigAverageOverBed` step on each per-chromosome fi ...
written 8 days ago by
Alex Reynolds ♦ 31k
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... Chromosome names have to match up to do operations. In other words, `1,chr1` will not match up with `chr1`, for example. Adjust your `awk` statement accordingly, so that you're not adding commas, numbers or other extraneous stuff to the chromosome field of `INPUT.bed`. ...
written 9 days ago by
Alex Reynolds ♦ 31k
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... That looks like a pretty unusual bed file, where the chromosomes do not look formatted correctly, and it isn't sorted in a typical way. What do the chromosome names in the bigWig file look like?
...
written 10 days ago by
Alex Reynolds ♦ 31k
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... A port of Linux compatible with the M1 is being worked on. More information here: https://www.patreon.com/marcan and here: https://asahilinux.org/ ...
written 11 days ago by
Alex Reynolds ♦ 31k
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Answer:
A: How to check size of genome?
... Reads will overlap, so you can't simply count the lengths of reads. To count the number of unique bases over reads per chromosome for assembly `hg38`, for example, using BEDOPS, bash, awk, and UCSC Kent utilities:
$ ASSEMBLY=hg38
$ bam2bed --reduced < reads.bam | bedmap --echo --bases-un ...
written 13 days ago by
Alex Reynolds ♦ 31k
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Comment:
C: Samtools Faidx Error Message
... Great point. I don't track what versions of dynamic libraries that tools use. One more argument in favor of static binaries. ...
written 15 days ago by
Alex Reynolds ♦ 31k
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Comment:
C: Samtools Faidx Error Message
... Perhaps some of the advice here might help for getting OpenSSL libraries installed and linked: https://gist.github.com/aklap/e885721ef15c8668ed0a1dd64d2ea1a7 ...
written 15 days ago by
Alex Reynolds ♦ 31k
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Answer:
A: Venn Diagrams with labels
... There is also [biovenn.nl][1].
[1]: http://biovenn.nl/ ...
written 16 days ago by
Alex Reynolds ♦ 31k
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... You could use a Python script to do this easily:
#!/usr/bin/env python
import sys
headers = None
idx = 0
for line in sys.stdin:
elems = line.rstrip().split('\t')
if idx == 0:
headers = elems
sys.stdout.write(line)
else:
...
written 18 days ago by
Alex Reynolds ♦ 31k
2
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... Get the total, summed length of the 318 sequences in your FASTA file, e.g. via https://www.danielecook.com/generate-fasta-sequence-lengths/
Set your `-maxsize` parameter to this value.
More explicitly, the output of the [aforementioned one-liner][1] can be quickly piped to a second `awk` statement ...
written 20 days ago by
Alex Reynolds ♦ 31k
Latest awards to Alex Reynolds
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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?
Good Answer
6 days ago,
created an answer that was upvoted at least 5 times.
For A: Vcf File --> Gene/Protein Mutation Information
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13 days ago,
created an answer that has been accepted.
For A: No PhyloP score for first stretch of chromosome?
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15 days ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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18 days ago,
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For A: No PhyloP score for first stretch of chromosome?
Epic Question
20 days ago,
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For Getting list of chromosome names from indexed BAM file
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For A: Sam To Bed File With Counter Column
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5 weeks ago,
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For A: Sam To Bed File With Counter Column
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For A: No PhyloP score for first stretch of chromosome?
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7 weeks ago,
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For A: No PhyloP score for first stretch of chromosome?
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8 weeks ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For Cubemaker - visualize three-dimensional datasets via the web
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9 weeks ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher
10 weeks ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
Teacher
3 months ago,
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For A: How To Intersect Two Tracks In Ucsc Table Browser And Get Fields From Both?
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For A: No PhyloP score for first stretch of chromosome?
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3 months 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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For Tips On Compiling And Using Meme 4.3 With A Sun Grid Engine Computation Cluster
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For A: Genomic coordinates for Cytogenetic bands with R
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