Moderator: Alex Reynolds
Alex Reynolds ♦ 24k
- Reputation:
- 24,210
- Status:
- Trusted
- Location:
- Seattle, WA USA
- Website:
- http://dropbit.com/
- Twitter:
- AlexReynolds
- Scholar ID:
- Google Scholar Page
- Last seen:
- 4 hours ago
- Joined:
- 8 years, 7 months 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
<prev
• 2,140 results •
page 1 of 214 •
next >
1
vote
3
answers
147
views
3
answers
Answer:
A: dna compression cod
... If you're strictly talking about generic DNA, you might look into the 2bit and nib formats: http://genome.ucsc.edu/FAQ/FAQformat.html#format7
Ignoring ambiguous bases, you can encode the four bases of DNA (A, C, G, T) with two binary bits like so:
A : 00
C : 01
G : 10
T : 11
Consi ...
written 15 hours ago by
Alex Reynolds ♦ 24k
1
vote
3
answers
105
views
3
answers
Answer:
A: perl compilation errors
... Break up that Perl one-liner into something you can debug line by line. ...
written 8 days ago by
Alex Reynolds ♦ 24k
1
vote
3
answers
166
views
3
answers
... To get an ad-hoc subset, you can use set operations in a Unix pipeline:
$ echo -e 'chr2\t1\t7' | bedops -e 1 foo.bed - | bedops --chop 1 - | bedmap --faster --echo --echo-map-id --delim "\t" - foo.bed | cut -f1,2,4 > answer.txt
The `--faster` option can be used here, as none of your example ...
written 9 days ago by
Alex Reynolds ♦ 24k
0
votes
4
answers
293
views
4
answers
Answer:
A: GREP: out of memory
... To have `grep` do exact-word matches from a file of strings, use `-w -F`:
$ grep -w -F -f 1.txt 2.gff > 3.gff
The `-w` option does word searches using regular expressions. The `-F` option modifies this to do exact-string matching.
Using `-w` on its own will consume a lot of memory, becaus ...
written 9 days ago by
Alex Reynolds ♦ 24k
0
votes
1
answer
78
views
1
answers
... Steps via `awk` and [BEDOPS][1].
Build a BED file of exons:
$ wget -qO- ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_28/gencode.v28.annotation.gtf.gz \
| gunzip -c - \
| awk '($3=="exon")' - \
| gtf2bed - \
| cut -f1-6 - \
> gencode ...
written 9 days ago by
Alex Reynolds ♦ 24k
3
votes
3
answers
166
views
3
answers
... If you want to use set operations:
$ bedops --chop 1 foo.bed | bedmap --faster --echo --echo-map-id --delim "\t" - foo.bed | cut -f1,2,4 > answer.txt ...
written 9 days ago by
Alex Reynolds ♦ 24k
1
vote
0
answers
93
views
0
answers
... Perhaps make notched box plots to more directly do comparisons of medians between two groups. https://www.jstor.org/stable/2683468?seq=1#page_scan_tab_contents ...
written 10 days ago by
Alex Reynolds ♦ 24k
2
votes
2
answers
108
views
2
answers
... Convert to BED via `convert2bed` helper scripts:
$ gff2bed < annotations.gff > annotations.bed
$ gff2bed < rmsk.gff > rmsk.bed
$ bam2bed < reads.bam > reads.bed
If you want at least X reads that overlap annotations that do not overlap repeatmasked regions:
$ X=12 ...
written 10 days ago by
Alex Reynolds ♦ 24k
0
votes
1
answer
125
views
1
answers
... To do this efficiently, you can use `bedops` and `bedmap` to calculate this over N files (N=57, in your case).
$ bedops -u A.bed B.bed ... N.bed > union.bed
$ bedops -m A.bed B.bed ... N.bed > merge.bed
$ bedmap --echo --mean --delim "\t" merge.bed union.bed > answer.bed
The f ...
written 11 days ago by
Alex Reynolds ♦ 24k
2
votes
2
answers
130
views
2
answers
... Look at the `seqLogo` package in Bioconductor. https://bioconductor.org/packages/release/bioc/html/seqLogo.html You could use the `ic` property of a `seqLogo` object: https://bioconductor.org/packages/release/bioc/vignettes/seqLogo/inst/doc/seqLogo.pdf
If you are comfortable with the command line, ...
written 13 days ago by
Alex Reynolds ♦ 24k
Latest awards to Alex Reynolds
Teacher
2 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?
Teacher
5 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?
Teacher
9 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
9 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
13 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
15 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
22 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
25 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
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
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
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
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
6 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
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?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: How to read fastq file with Python
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: How to read fastq file with Python
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?
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?
Scholar
8 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?
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?
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1051 users visited in the last hour