User: colindaven
colindaven • 2.6k
- Reputation:
- 2,620
- Status:
- Trusted
- Location:
- Hannover Medical School
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 hours ago
- Joined:
- 4 years, 7 months ago
- Email:
- c*********@hotmail.com
Staff Scientist Bioinformatics
2
votes
3
answers
152
views
3
answers
... Have a look at https://github.com/shenwei356/taxonkit , I think it's exactly what you need
...
written 6 weeks ago by
colindaven • 2.6k
1
vote
1
answer
109
views
1
answers
Answer:
A: filtering alignned seqeunces
... A more standard way to do this would be
1. convert SAM to BAM with BAI index
2. run samtools idxstats x.bam
3. alternative: run samtools stats x.bam
This would give you the stats including number of reads aligned to each reference as a text file. Very useful if you have many references. ...
written 7 weeks ago by
colindaven • 2.6k
1
vote
4
answers
210
views
4
answers
... Try biopython, from memory they use delimiters such as space to differentiate the ID from the name or annotation fields. It might be helpful to use sed etc in Linux to modify the fasta headers to get the ID and Name to "stick together", depending on what you want to do.
You are right though, fasta ...
written 7 weeks ago by
colindaven • 2.6k
0
votes
1
answer
212
views
1
answers
... If you have related genomes, potentially ref based scaffolding tools like this are useful.
https://github.com/malonge/RaGOO
https://github.com/combogenomics/medusa ...
written 10 weeks ago by
colindaven • 2.6k
0
votes
1
answer
104
views
1
answers
... You can have a look at MAKER for annotation.
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-491
The DFAM database might help for data, but I don't know if that covers your insects.
https://dfam.org/
Perhaps for large scale projects like this you need to apply for comput ...
written 10 weeks ago by
colindaven • 2.6k
0
votes
5
answers
466
views
5
answers
... I use the server version exclusively. It's not too hard to set up and you want your software where the data lives to avoid endless unnecessary data transfers. ...
written 10 weeks ago by
colindaven • 2.6k
0
votes
5
answers
466
views
5
answers
... I'm a big fan of JBrowse. I prefer it to the likes of IGB and IGV because of the much faster loading times for big BAMs. It also allows you to structure information for users so they can explore data integration.
I haven't tried JBrowse2 yet, but its on my list and brand new in 2020. ...
written 11 weeks ago by
colindaven • 2.6k
0
votes
0
answers
1.9k
views
0
answers
... We're running a ca 1000 core SLURM cluster on Ubuntu. The LTS are very good, docs are great. There's another cluster here running on RHEL but that's from IT. We had a look at Debian but far less docs, and even essential programs like ls can be subtly different. ...
written 11 weeks ago by
colindaven • 2.6k
0
votes
0
answers
132
views
0
answers
... You'll probably get a good answer on the canu github repo. ...
written 11 weeks ago by
colindaven • 2.6k
1
vote
1
answer
146
views
1
answers
... This post might be relevant for you:
https://www.biostars.org/p/77756/ ...
written 11 weeks ago by
colindaven • 2.6k
Latest awards to colindaven
Teacher
27 days ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Bioinformatics PhD position in Next Generation Sequencing analysis
Appreciated
3 months ago,
created a post with more than 5 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
5 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Scholar
5 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Scholar
6 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Scholar
6 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
Scholar
10 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
10 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Using the MinION MinKNOW software on Ubuntu 1604
Scholar
14 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
16 months ago,
created an answer with at least 3 up-votes.
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
17 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Appreciated
17 months ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Popular Question
18 months ago,
created a question with more than 1,000 views.
For bbmap callvariants.sh on pacbio
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Commentator
19 months ago,
created a comment with at least 3 up-votes.
For C: is fortran still used in bioinformatics?
Scholar
19 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: 2869 users visited in the last hour