Moderator: Philipp Bayer
Philipp Bayer ♦ 5.6k
- Reputation:
- 5,610
- Status:
- Trusted
- Location:
- Australia/Perth/UWA
- Twitter:
- PhilippBayer
- Last seen:
- 9 hours ago
- Joined:
- 6 years, 4 months ago
- Email:
- p*********@googlemail.com
Post-Doc bioinformatics at the University of Western Australia, co-founder openSNP.org
Posts by Philipp Bayer
<prev
• 453 results •
page 1 of 46 •
next >
0
votes
0
answers
61
views
0
answers
Comment:
C: MCScanX empty collinearity file.
... You should have an 'edit' button where you can delete the whole question - but to answer your question, it looks like there's something wrong with the alignments file, the tandem duplications file worked fine but the inter-species comparison is broken, perhaps because the IDs in the gff file are dif ...
written 11 hours ago by
Philipp Bayer ♦ 5.6k
0
votes
2
answers
182
views
2
answers
Comment:
C: Visualizing contig alignment
... I usually remove small contigs (<10kb) because these will only add chaos to the graph anyway. ...
written 8 days ago by
Philipp Bayer ♦ 5.6k
2
votes
2
answers
182
views
2
answers
Answer:
A: Visualizing contig alignment
... Are dotplots not an option?
Minidot is very fast, but in my experience doesn't work that great with 'bad' assemblies: https://github.com/thackl/minidot
Symap is a bit older and slower, but works better with low quality assemblies (again, in my experience), and can also make a circular plot http:// ...
written 16 days ago by
Philipp Bayer ♦ 5.6k
0
votes
3
answers
140
views
3
answers
... Another suggestion:
Run Trimmomatic on your data with the TOPHRED33 flag, see whether that'll change your quality scores. ...
written 5 weeks ago by
Philipp Bayer ♦ 5.6k
1
vote
1
answer
111
views
1
answers
... Things I would try:
- check whether the input file is broken (use `tail` to check the end)
- remove small contigs from the assembly (for example, `bioawk -c fastx '{ if(length($seq) > 1000) { print ">"$name; print $seq }}' sandalnew.fa > filtered_sandalnew.fa` )
- recompile augustus via ...
written 6 weeks ago by
Philipp Bayer ♦ 5.6k
3
votes
1
answer
180
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 8 weeks ago by
Philipp Bayer ♦ 5.6k
0
votes
1
answer
164
views
1
answers
... Tell them 'congratulations' from me, it's a really cool paper! ...
written 10 weeks ago by
Philipp Bayer ♦ 5.6k
0
votes
1
answer
164
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 10 weeks ago by
Philipp Bayer ♦ 5.6k
4
votes
1
answer
293
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 11 weeks ago by
Philipp Bayer ♦ 5.6k
0
votes
2
answers
162
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 12 weeks ago by
Philipp Bayer ♦ 5.6k
Latest awards to Philipp Bayer
Scholar
6 days ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Scholar
15 days ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Popular Question
23 days ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Good Answer
5 weeks ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: Quickest way to extract subset of reads from huge fastq file
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Scholar
3 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?
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?
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Commentator
9 months ago,
created a comment with at least 3 up-votes.
For C: Good Habit for Bioinformatics Analyst or Scientist
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For A: New To Python And Putty: Help!
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.
Teacher
9 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!
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
10 months ago,
created a question with more than 1,000 views.
For How does MAKER decide which proteins go into the final output?
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: How Can I Remove My Post From Biostar.
Appreciated
11 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: 1435 users visited in the last hour