User: Jeffin Rockey
Jeffin Rockey • 720
- Reputation:
- 720
- Status:
- Trusted
- Location:
- Karimannoor
- Last seen:
- 10 hours ago
- Joined:
- 2 years, 4 months ago
- Email:
- j***********@hotmail.com
Posts by Jeffin Rockey
<prev
• 96 results •
page 1 of 10 •
next >
0
votes
1
answer
126
views
1
answers
... John,
Confirmed. With -sorted itself it is slow.
Jeffin ...
written 13 hours ago by
Jeffin Rockey • 720
0
votes
1
answer
126
views
1
answers
... Alex,
Even without --faster bedops was significantly faster and that speedup itself was sufficient. But the difference in results of --element-of 1 from bedtools intersect is what held me back from using bedops. ...
written 1 day ago by
Jeffin Rockey • 720
0
votes
1
answer
126
views
1
answers
... Thanks Alex. I shall try with the mentioned options and see if they can be used instead. ...
written 1 day ago by
Jeffin Rockey • 720
0
votes
1
answer
126
views
1
answers
... John,
I remember so. Let me cross check again. Shall confirm on this at the earliest. ...
written 1 day ago by
Jeffin Rockey • 720
0
votes
1
answer
126
views
1
answers
... When I tried to parallelize bedtools, they are in fact individually slowing down effectively nullifying the expected advantage. I checked in different servers[256 GB], but this behaviour is recurring, may be something to do with RAM. ...
written 1 day ago by
Jeffin Rockey • 720
1
vote
1
answer
126
views
1
answers
... There are 10+ methylome bedfiles which have the positions of methylated bases. They are obtained through bwa-meth followed by methyldackel followed by conversion to bed. Roughly each file has 80,000,000+ entries. I was trying to intersect these with gene features like exons. The count came as expect ...
written 1 day ago by
Jeffin Rockey • 720
2
votes
1
answer
126
views
7 follow
1
answer
... What are the alternative tools available which can do what `bedtools intersect` does? ...
written 1 day ago by
Jeffin Rockey • 720
• updated
1 day ago by
Alex Reynolds ♦ 26k
0
votes
1
answer
88
views
1
answers
... Do sorting of both the files with sort -V giving appropriate columns (e.g,1-3 in the given file.bed) and then try . ...
written 2 days ago by
Jeffin Rockey • 720
0
votes
1
answer
158
views
1
answers
Answer:
C: ddRAD analysis pipelines
... Resolved now.
The reason was completely unexpected.
The enzyme cut-site sequence I provided was incorrect. So in filtering step most of the reads did not pass(zero for all most all samples). This caused the error downstream at step6.
Once I gave the correct cut-site it worked as expected.Took ...
written 6 days ago by
Jeffin Rockey • 720
1
vote
3
answers
103
views
3
answers
... Would be easier through conda.
Download and run https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh if 64 bit.
Then exit and re-login for ~/.bashrc entries to take effect or run source ~/.bashrc instead.
Then install cut adapt with command `conda install -c bioconda cutadapt`
( ...
written 9 days ago by
Jeffin Rockey • 720
Latest awards to Jeffin Rockey
Teacher
12 weeks ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Appreciated
11 months ago,
created a post with more than 5 votes.
For A: SAM FLAG for primary alignments, secondary alignments and what's their relations
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Faster way to get coverage per base
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1675 users visited in the last hour