Moderator: Philipp Bayer
Philipp Bayer ♦ 5.9k
- Reputation:
- 5,930
- Status:
- Trusted
- Location:
- Australia/Perth/UWA
- Twitter:
- PhilippBayer
- Last seen:
- 2 hours ago
- Joined:
- 6 years, 10 months ago
- Email:
- p*********@googlemail.com
Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
<prev
• 477 results •
page 1 of 48 •
next >
0
votes
1
answer
131
views
1
answers
... I suggest the Hisat2/Stringtie/Ballgown pipeline, see Dave Tang's blogpost: https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/
For read cleaning and adapter trimming, have a look at fastp: https://github.com/OpenGene/fastp ...
written 10 days ago by
Philipp Bayer ♦ 5.9k
0
votes
1
answer
61
views
1
answers
... How are you running scipio?
Looking at the manual, you run scipio with your amino acid fasta file, not your gff file:
scipio.1.4.pl --blat_output=prot.vs.genome.psl genome.fa proteins.aa > scipio.yaml # takes ~7m
In that case, your input amino acid file has stop codons, which are normall ...
written 14 days ago by
Philipp Bayer ♦ 5.9k
2
votes
2
answers
135
views
2
answers
... I have an annotation for a genome assembly in scaffold format in gff3/fasta format - someone else has ordered these scaffolds into pseudomolecules, so now I want to move the 'old' annotation in gff3 format from their scaffold positions into the pseudomolecules' position.
I could write a script to ...
written 14 days ago by
Philipp Bayer ♦ 5.9k
• updated
13 days ago by
Carambakaracho • 760
0
votes
1
answer
173
views
1
answers
... If you really want to use time as the condition, yes it would be a bit like your table above -
you'd have one table with time points A and B only, one table with time points A and C only, one with A and D, etc., B and C, B and D, etc. pp.,
Sure you can compare the first day with the other 6 days, ...
written 17 days ago by
Philipp Bayer ♦ 5.9k
0
votes
1
answer
173
views
1
answers
... I think what you're looking for is a time series analysis - there are some older biostars threads around this (for example https://www.biostars.org/p/125010/ ), here's a review paper which compares a bunch of MATLAB/R packages and finds that ImpulseDE2 works best for them: https://academic.oup.com/b ...
written 18 days ago by
Philipp Bayer ♦ 5.9k
2
votes
0
answers
1.1k
views
0
answers
... Hi Eshwari! I'm afraid this post is 3 years old, our GSoC project ended a long time ago!
However, this round of GSoC will be announced in 3 weeks: https://summerofcode.withgoogle.com/?csw=1
I'm sure there'll be many bioinformatics projects again this year, good luck!! ...
written 19 days ago by
Philipp Bayer ♦ 5.9k
0
votes
1
answer
148
views
1
answers
... As an aside, if you're with an Australian institution you can use EMBL-ABR's data chaperoning service, they will do this work for you : https://www.embl-abr.org.au/data-chaperoning/ ...
written 4 weeks ago by
Philipp Bayer ♦ 5.9k
0
votes
1
answer
212
views
1
answers
... Not really, no - Kraken2 is so new that I haven't seen any benchmarks yet. Kraken1 was slower but more accurate (IIRC) ...
written 7 weeks ago by
Philipp Bayer ♦ 5.9k
2
votes
1
answer
212
views
1
answers
... Looks like you're looking for a metagenomics tool - tools like [Kraken 2][1] or [Centrifuge][2] are much faster for what you want to do
[1]: https://ccb.jhu.edu/software/kraken2/
[2]: https://ccb.jhu.edu/software/centrifuge/ ...
written 7 weeks ago by
Philipp Bayer ♦ 5.9k
3
votes
1
answer
146
views
1
answers
... Swiss-Prot is a manually curated database of proteins, available here: https://www.uniprot.org
Smith-Waterman is one of the more basic bioinformatics alignments for *local* sequence alignments, which is an optional setting in BLAST. Smith-Waterman is much more slower than BLAST's standard algorithm ...
written 7 weeks ago by
Philipp Bayer ♦ 5.9k
Latest awards to Philipp Bayer
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
10 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?
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
5 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Scholar
5 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Popular Question
5 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
7 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
8 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Commentator
14 months ago,
created a comment with at least 3 up-votes.
For C: Good Habit for Bioinformatics Analyst or Scientist
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Good Answer
14 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1894 users visited in the last hour