User: colindaven
colindaven • 1.9k
- Reputation:
- 1,950
- Status:
- Trusted
- Location:
- Hannover Medical School
- Last seen:
- 11 hours ago
- Joined:
- 3 years, 7 months ago
- Email:
- c*********@hotmail.com
Posts by colindaven
<prev
• 321 results •
page 1 of 33 •
next >
2
votes
0
answers
75
views
0
answers
... Try a newer version of samtools like 1.7+
The you can do what @lieven.sterck recommended above, maybe idxstats will be most helpful.
Program: samtools (Tools for alignments in the SAM format)
Version: 1.7 (using htslib 1.7)
Usage: samtools [options]
Commands:
...
written 15 hours ago by
colindaven • 1.9k
0
votes
1
answer
81
views
1
answers
Answer:
A: how to find haplotype of SNPs
... If you have short reads (eg not Pacbio/Nanopore) phasing results are likely to be very, very poor, as no long range information (long reads) are available. ...
written 1 day ago by
colindaven • 1.9k
0
votes
2
answers
153
views
2
answers
... Clair also has a good reputation in addition to Longshot https://www.biorxiv.org/content/10.1101/2020.02.07.939322v1?ct=
However I have Longshot https://github.com/pjedge/longshot quite easy to install and run, as long as you can get over the initial RUST hurdles. Fascinatingly, it's the first tool ...
written 1 day ago by
colindaven • 1.9k
0
votes
2
answers
196
views
2
answers
Answer:
A: Maker usage and tBLASTn
... Maker is good - but as lieven.sterck says, it is a genome annotation program. It does work and is not too tricky to configure.
Do you want to annotate a genome and create a geneset ? ...
written 1 day ago by
colindaven • 1.9k
0
votes
0
answers
75
views
0
answers
... You have included almost no information in your post so it is impossible to help you. Retry ? What did you align to ? Did you align data ? ...
written 1 day ago by
colindaven • 1.9k
0
votes
0
answers
77
views
0
answers
... You may not have enough RAM (how much do you have ?). Use `htop` or `free -g` to find out.
If you don't have enough, the mapping step might also not work. ...
written 10 days ago by
colindaven • 1.9k
1
vote
1
answer
132
views
1
answers
Comment:
C: install bcl2fastq
... Try creating a file like this globalenv and adding it to your /home/YOURUSER/.bashrc file
eg at the end of my .bashrc file I write this:
$ cat ~/.bashrc
source /mnt/ngsnfs/globalenv/globalenv
For more details check
https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-pa ...
written 14 days ago by
colindaven • 1.9k
0
votes
1
answer
114
views
1
answers
... Yep, it works, yep, they should use other data - but that wasn't the question.
I'd probably trust it for alignments, but not for SNV calls as you're not using the colour space information. ...
written 15 days ago by
colindaven • 1.9k
0
votes
1
answer
132
views
1
answers
Comment:
C: install bcl2fastq
... For the second question, you need to add bcl2fastq to your PATH, eg something like
https://askubuntu.com/questions/60218/how-to-add-a-directory-to-the-path
...
written 15 days ago by
colindaven • 1.9k
0
votes
1
answer
114
views
1
answers
... Because the reads were aligned against a reference, you can just use BAM 2 fastq methods to extract the sequences. That way you get a FASTQ and avoid colourspace altogether, which I would not recommend using for RNA-seq projects in any case.
You can use a modern samtools for this:
samtools fa ...
written 15 days ago by
colindaven • 1.9k
Latest awards to colindaven
Scholar
8 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
4 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Teacher
5 months ago,
created an answer with at least 3 up-votes.
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
Appreciated
5 months ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Popular Question
6 months ago,
created a question with more than 1,000 views.
For bbmap callvariants.sh on pacbio
Teacher
7 months ago,
created an answer with at least 3 up-votes.
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
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: is fortran still used in bioinformatics?
Scholar
7 months ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: Gene annotation pipeline for bacteria
Commentator
8 months ago,
created a comment with at least 3 up-votes.
For C: is fortran still used in bioinformatics?
Teacher
8 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
Guru
12 months ago,
received more than 100 upvotes.
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Gene annotation pipeline for bacteria
Scholar
12 months ago,
created an answer that has been accepted.
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
Scholar
13 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
Voter
2.1 years ago,
voted more than 100 times.
Centurion
2.2 years ago,
created 100 posts.
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Gene annotation pipeline for bacteria
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
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: 1197 users visited in the last hour