Moderator: Philipp Bayer

gravatar for Philipp Bayer
Philipp Bayer6.7k
Reputation:
6,680
Status:
Trusted
Location:
Australia/Perth/UWA
Twitter:
PhilippBayer
Last seen:
1 day, 11 hours ago
Joined:
8 years, 3 months ago
Email:
p*********@googlemail.com

Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org

Posts by Philipp Bayer

<prev • 535 results • page 1 of 54 • next >
0
votes
2
answers
3.1k
views
2
answers
Comment: C: Error in Calculation of Ka/Ks value using Ka/Ks calculator
... 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 5 weeks ago by Philipp Bayer6.7k
2
votes
1
answer
164
views
1
answers
Comment: C: Multiple Sequence Alignment for Full length genomes
... 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 7 weeks ago by Philipp Bayer6.7k
0
votes
1
answer
166
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 7 weeks ago by Philipp Bayer6.7k
1
vote
1
answer
219
views
1
answers
Answer: A: Getting assembly from sam/bam file
... 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 6 months ago by Philipp Bayer6.7k
0
votes
0
answers
588
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 6 months ago by Philipp Bayer6.7k
0
votes
1
answer
1.9k
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 7 months ago by Philipp Bayer6.7k
0
votes
1
answer
1.9k
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 7 months ago by Philipp Bayer6.7k
1
vote
1
answer
243
views
1
answers
Comment: C: Scaleable trimming of GenBank sequences?
... 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 7 months ago by Philipp Bayer6.7k
0
votes
1
answer
243
views
1
answers
Comment: C: Scaleable trimming of GenBank sequences?
... (A few minutes later: Current best pipeline I can find is MAFFT/MUSCLE with gaps turned off, followed by trimAl, in a wrapper script to parallelise? curious to hear more!) ...
written 7 months ago by Philipp Bayer6.7k
3
votes
1
answer
243
views
1
answer
Scaleable trimming of GenBank sequences?
... I'm trying to automate the building of a reference database for DADA2. As such I'm using esearch to download ~200k fasta sequences for my search term of one gene from GenBank. Many GenBank sequences are joined-up sequences of several genes, and I'd like to trim those unnecessary genes away in order ...
alignment written 7 months ago by Philipp Bayer6.7k

Latest awards to Philipp Bayer

Popular Question 27 days ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Great Question 4 weeks ago, created a question with more than 5,000 views. For What Is One Book Every Bioinformatician Should Read?
Appreciated 3 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Popular Question 6 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 6 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Scholar 7 months ago, created an answer that has been accepted. For A: Long reads Assembly Algorithms
Appreciated 8 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Scholar 8 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 10 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: New To Python And Putty: Help!
Appreciated 11 months ago, created a post with more than 5 votes. For A: New To Python And Putty: Help!
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Great Question 11 months ago, created a question with more than 5,000 views. For What Is One Book Every Bioinformatician Should Read?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Popular Question 13 months ago, created a question with more than 1,000 views. For How does MAKER decide which proteins go into the final output?
Scholar 13 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Appreciated 13 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!
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Good Habit for Bioinformatics Analyst or Scientist
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Scholar 13 months ago, created an answer that has been accepted. For A: Quickest way to extract subset of reads from huge fastq file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How Can I Remove My Post From Biostar.
Librarian 14 months ago, created a post with more than 10 bookmarks. For What Is One Book Every Bioinformatician Should Read?
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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1369 users visited in the last hour