Moderator: Philipp Bayer
Philipp Bayer ♦ 6.8k
- Reputation:
- 6,790
- Status:
- Trusted
- Location:
- Australia/Perth/UWA
- Twitter:
- PhilippBayer
- Last seen:
- 1 week, 2 days ago
- Joined:
- 8 years, 6 months ago
- Email:
- p*********@googlemail.com
Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
<prev
• 537 results •
page 1 of 54 •
next >
6
votes
7
answers
970
views
7
answers
... As a bioinformatician you have a (currently) very valuable skill-sets. People will seek you out, hoping that you'll do their analysis for them. I have been burned by this because people don't know what you can and cannot do, so they come to you with insufficient data, with a vaguely defined biologic ...
written 4 weeks ago by
Philipp Bayer ♦ 6.8k
0
votes
2
answers
5.3k
views
2
answers
... This would be its own good question but yeah, right now I lean towards not running RepeatMasker via MAKER, but instead later remove proteins tha tare X% covered by known repeats or contain transposase related domains ...
written 5 weeks ago by
Philipp Bayer ♦ 6.8k
0
votes
2
answers
3.3k
views
2
answers
... I edited your comment to make the code look nicer,
I don't know perl much, but isn't your input already a clustalw alignment? I don't understand what your input file is, there are many ways to store an orthologous gene family? ...
written 3 months ago by
Philipp Bayer ♦ 6.8k
2
votes
1
answer
210
views
1
answers
... Another option:
Rob Lanfear has a repo up where he has already run the MSA https://github.com/roblanf/sarscov2phylo/
He uses MAFFT too in this script https://github.com/roblanf/sarscov2phylo/blob/master/scripts/global_profile_alignment.sh ...
written 4 months ago by
Philipp Bayer ♦ 6.8k
0
votes
1
answer
232
views
1
answers
Answer:
A: KaryoploteR for copy number
... I think you switched up your variables, custom.genome needs the actual chromosome lengths and no other measurements, the table you have there needs to be given to kpPlotDensity(), not to plotKarytyope()
Have a look at this code I wrote a while ago which uses custom.genome too: https://github.com/ph ...
written 4 months ago by
Philipp Bayer ♦ 6.8k
1
vote
1
answer
326
views
1
answers
... I think it's probably best if you use RaGOO for that - https://github.com/malonge/RaGOO
It runs minimap2 using your contigs and a reference assembly and then orders the contigs based on the alignment. You may have to rerun your alignments, I don't know whether you can give it the sam file directly. ...
written 8 months ago by
Philipp Bayer ♦ 6.8k
0
votes
0
answers
852
views
0
answers
Comment:
C: PLINK --allow-extra-chr error
... Have you tried using --allow-extra-chr without the 0?
Have you tried looking at line 938485, 938486, 938487 to see whether these lines are just broken somehow? ...
written 9 months ago by
Philipp Bayer ♦ 6.8k
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: Brassica napus reference genome
... Hi, here's a different fixed version: https://cloudstor.aarnet.edu.au/plus/s/hPwZU13L1Hx2nFM
I re-added the missing gene-lines and sorted by chromosome and position ...
written 10 months ago by
Philipp Bayer ♦ 6.8k
0
votes
1
answer
2.0k
views
1
answers
Comment:
C: Brassica napus reference genome
... Hmmmm can't find it myself any more :O I got it on an old laptop?
I'll re-create the file asap ...
written 10 months ago by
Philipp Bayer ♦ 6.8k
1
vote
1
answer
273
views
1
answers
... Amazing idea, I hadn't even thought of soft-clipping! I've currently written a relatively slow script that does what I describe in the OP post, after that I'll give BWA or similar a try, which is probably WAY faster, thanks for the idea!!
Edit: FWIW, here's the simple script I ended up using - ran ...
written 10 months ago by
Philipp Bayer ♦ 6.8k
Latest awards to Philipp Bayer
Appreciated
4 weeks ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For A: Directions In Bioinformatics And Web-Based Data Visualization: Revisiting Javasc
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Long reads Assembly Algorithms
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Directions In Bioinformatics And Web-Based Data Visualization: Revisiting Javasc
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Great Question
3 months ago,
created a question with more than 5,000 views.
For What Is One Book Every Bioinformatician Should Read?
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Popular Question
9 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Scholar
9 months ago,
created an answer that has been accepted.
For A: Long reads Assembly Algorithms
Scholar
9 months ago,
created an answer that has been accepted.
For A: Long reads Assembly Algorithms
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Scholar
10 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Good Answer
13 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Appreciated
13 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Great Question
14 months ago,
created a question with more than 5,000 views.
For What Is One Book Every Bioinformatician Should Read?
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Popular Question
15 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Scholar
15 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Good Answer
16 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Appreciated
16 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Teacher
16 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Commentator
16 months ago,
created a comment with at least 3 up-votes.
For C: Good Habit for Bioinformatics Analyst or Scientist
Scholar
16 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1405 users visited in the last hour