User: colindaven
colindaven • 2.3k
- Reputation:
- 2,260
- Status:
- Trusted
- Location:
- Hannover Medical School
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 6 hours ago
- Joined:
- 4 years ago
- Email:
- c*********@hotmail.com
Staff Scientist Bioinformatics
Posts by colindaven
<prev
• 361 results •
page 1 of 37 •
next >
0
votes
1
answer
127
views
1
answers
... Wow, the FASTQ from this with all set to 30 or 3 sounds ridiculously bad. It also would mark ALL long read data, both from Nanopore and Pacbio, as "reject" and give FASTQ out with quality values of 3. Why ? Because long read data is generally quality 8-15 at present. Great.
I didn't know NCBI was ...
written 6 days ago by
colindaven • 2.3k
0
votes
1
answer
70
views
1
answers
... You can try calling ORFs / genes in each and doing bidirectional blast to produce a CSV output, eg with proteinortho.
https://www.biostars.org/p/359736/#359814
Alternatively, you could look at BUSCO which would be the more standard approach. ...
written 16 days ago by
colindaven • 2.3k
0
votes
1
answer
74
views
1
answers
Answer:
A: Filtering microbial variants
... You should be able to find a lot of information about this already on this site. What research have you done ?
Also, I prefer multisample SNV calling, so you get a VCF with columns for each sample. This makes filtering a lot easier.
Finally, I prefer to filter in Galaxy using eg SnpSift Filter and ...
written 16 days ago by
colindaven • 2.3k
0
votes
0
answers
80
views
0
answers
... Perhaps this would have helped with the names and lengths somewhat faster. Then adapt to BED format
samtools faidx your.fasta
cat your.fasta.fai
...
written 17 days ago by
colindaven • 2.3k
1
vote
2
answers
85
views
2
answers
... We find adapters in genomes all the time which is terrible for metagenomics.
This simple tool might help you to at least diagnose your problem and or replace the adapters with NNNs https://github.com/colindaven/blacklister
Try additional adapter trimmers like
-trimmomatic
-fastp
and after adapte ...
written 17 days ago by
colindaven • 2.3k
0
votes
2
answers
605
views
2
answers
... It's not really intended to answer your question, and you've probably solved this by now, but our pipeline can do the alignment and your intended normalization (including number of reads and genome length):
https://github.com/MHH-RCUG/Wochenende
Seeing as you have a custom output, you'll need to ...
written 17 days ago by
colindaven • 2.3k
0
votes
73
answers
33k
views
73
answers
... Yeah, the people who conceived of that were utterly brilliant usability specialists. ...
written 4 weeks ago by
colindaven • 2.3k
1
vote
8
answers
2.4k
views
8
answers
... ChIP-seq is very difficult. I'd do this over several cycles in house if possible first to test antibodies and workflow. At our core we do multiple iterations with the customer before we get good results, and then we go to a bigger sequencer for higher throughput.
I would never recommend just sendi ...
written 8 weeks ago by
colindaven • 2.3k
1
vote
1
answer
101
views
1
answers
... Divide up the fasta using a script (there are various splitfasta style scripts out there in the world) then use the linux tool `cat` to concatenate the individual chromosomes including your new one back together.
...
written 8 weeks ago by
colindaven • 2.3k
1
vote
1
answer
132
views
1
answers
... Theres' a tool called **vt** (available via bioconda) which can do very nice summaries of vcf files. ...
written 8 weeks ago by
colindaven • 2.3k
Latest awards to colindaven
Appreciated
11 weeks ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
11 weeks ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Using the MinION MinKNOW software on Ubuntu 1604
Scholar
6 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
9 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Scholar
9 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Popular Question
11 months ago,
created a question with more than 1,000 views.
For bbmap callvariants.sh on pacbio
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: is fortran still used in bioinformatics?
Scholar
12 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Appreciated
12 months ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: is fortran still used in bioinformatics?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Guru
17 months ago,
received more than 100 upvotes.
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Scholar
17 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
17 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Scholar
18 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 987 users visited in the last hour