Moderator: Philipp Bayer
Philipp Bayer ♦ 5.5k
- Reputation:
- 5,530
- Status:
- Trusted
- Location:
- Australia/Perth/UWA
- Twitter:
- PhilippBayer
- Last seen:
- 6 hours ago
- Joined:
- 6 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
• 448 results •
page 1 of 45 •
next >
3
votes
1
answer
81
views
1
answers
Answer:
A: sorting a BAM file
... That seems to be a very strange read, how can it have a MAPQ > 0?
Anyway, you can either try `samtools sort -n` to sort by name, or try setting PICARD's VALIDATION_STRINGENCY to 'lenient', so for example
java -jar picard.jar SortSam I=your_input O=your_sorted_output VALIDATION_STRINGENCY=L ...
written 9 hours ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
76
views
1
answers
... Tell them 'congratulations' from me, it's a really cool paper! ...
written 16 days ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
76
views
1
answers
... Same for me, lack of coverage so no peak, I've never seen anything else myself.
There's an unlikely chance that it's a highly fragmented genome, see Suppl. Figure 3 in ['The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes'][1]. But again, unlikely.
[1]: https://www ...
written 16 days ago by
Philipp Bayer ♦ 5.5k
4
votes
1
answer
152
views
1
answers
Answer:
A: fasta to gff3
... There are numerous sources for gff3 files, it always depends on which organism you work with - Ensembl has many annotations in gff3 files, one example: http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
I'm not sure I understand your second question. A fasta file contains a whole genome asse ...
written 25 days ago by
Philipp Bayer ♦ 5.5k
0
votes
2
answers
103
views
2
answers
... There are many 'best practises' papers by now, the exact paper depends on your species (bacterium? plant?) and your technology (2nd generation? 3rd generation? Hybrid? 10x?)
Ten steps to get started in Genome Assembly and Annotation https://f1000research.com/articles/7-148/v1
A beginner’s guide to ...
written 27 days ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
178
views
1
answers
... I think the fast.ai community is the nicest one (but very few bioinformaticians from what I saw)
http://forums.fast.ai/
Their course is the best one I've seen on machine learning but very video-based which may not work for you, not sure! ...
written 5 weeks ago by
Philipp Bayer ♦ 5.5k
2
votes
1
answer
140
views
1
answers
Answer:
A: agriGO no longer available?
... I guess they turned off agriGO v1 (yours, paper from 2010) and left only agriGO v2 (paper from 2017) up? http://systemsbiology.cau.edu.cn/agriGOv2/
Especially for GO annotation I would always use the newest data possible - see for example https://www.nature.com/articles/s41598-018-23395-2 ...
written 6 weeks ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
4.2k
views
1
answers
... You can use
df -h
to see how much space you have left on each device.
There's a chance that the mysql process is not allowed to write to the folder with 613G, so look at the rights of that folder using `ls -lah` ...
written 6 weeks ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
4.2k
views
1
answers
... Your hard-drive is full, delete unnecessary stuff :)
...
written 6 weeks ago by
Philipp Bayer ♦ 5.5k
0
votes
1
answer
4.2k
views
1
answers
... The name of one or more genes are too long for the database!
Two ways to fix this:
- write a small script (using Bopython or Bioperl) that cuts off the names of your IDs to below 60 characters
- in the OrthoMCL script orthomclInstallSchema, change these two lines:
QUERY_ID ...
written 7 weeks ago by
Philipp Bayer ♦ 5.5k
Latest awards to Philipp Bayer
Scholar
9 hours ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Teacher
9 hours ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
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
3 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
4 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.
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: Good Habit for Bioinformatics Analyst or Scientist
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Good Answer
7 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Appreciated
7 months ago,
created a post with more than 5 votes.
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.
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Appreciated
7 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
Popular Question
8 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Teacher
8 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.
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: New To Python And Putty: Help!
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
9 months ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
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?
Appreciated
10 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: 633 users visited in the last hour