Moderator: finswimmer
finswimmer ♦ 2.7k
- Reputation:
- 2,740
- Status:
- Trusted
- Location:
- Germany
- Last seen:
- an hour ago
- Joined:
- 1 year, 3 months ago
- Email:
- f***********@gmail.com
Posts by finswimmer
<prev
• 473 results •
page 1 of 48 •
next >
1
vote
1
answer
43
views
1
answers
... Hello,
you could use `ggf2bed` from [BEDOPS][1]
$ gff2bed < foo.gff3 > foo.bed
fin swimmer
[1]: http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gff2bed.html ...
written 5 hours ago by
finswimmer ♦ 2.7k
1
vote
0
answers
72
views
0
answers
... Hello,
I don't know whether the restriction mentioned in this [post][1] still exists. So be careful.
fin swimmer
[1]: https://www.biostars.org/p/135900/#135902 ...
written 6 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
72
views
0
answers
... Hi de.mecquenem.ninon,
This reply is better suited as a comment on Carambakaracho's answer. Answers should ONLY be used to respond to the original question at the top of this page. I moved your post to a comment. But as you see this is not perfect.
fin swimmer ...
written 6 hours ago by
finswimmer ♦ 2.7k
0
votes
3
answers
5.7k
views
3
answers
... Hello Hakubi and welcome to biostars,
your post is better placed as a comment. To do this please use the `ADD COMMENT` button below the post you like to reply to. Answers should only be used to respond to the original question at the top of this page and should answer the question as best as possib ...
written 8 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
67
views
0
answers
... > It is because I used, nohup?
Yes, you are right. From `nohup --help`:
If standard error is a terminal, it is redirected to standard output.
I think you can repair your sam file by removing all lines that starts with `[`
grep -v "^[" SRR6876052_mem.sam > repaired.sam ...
written 9 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
67
views
0
answers
... You're correct, These status message shouldn't be in the sam file. In the command you gave above I cannot see why this happens.
Standard questions at this point: What version of bwa are you using? Which OS are you using?
fin swimmer ...
written 9 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
67
views
0
answers
... To get the whole header:
grep "@" SRR6876052_mem.sam
To get the first 10 lines that are not the header:
grep -m 10 -v "^@" SRR6876052_mem.sam ...
written 10 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
67
views
0
answers
... Hello again,
those lines starting with `@` are the header lines. Beside this we need the first few lines that doesn't start by `@.`
fin swimmer
BTW: It's better to use the `code` formating button for file contents as well. ...
written 10 hours ago by
finswimmer ♦ 2.7k
0
votes
0
answers
67
views
0
answers
... Hello shuksi,
could you please post the first lines of your sam file? How have you produced this file?
fin swimmer ...
written 10 hours ago by
finswimmer ♦ 2.7k
2
votes
2
answers
154
views
2
answers
... Here the new script based on the [new criterias][1]:
https://gist.github.com/finswimmer/7b540d695fede0fdb10120d53afab2ca
Output now looks like this:
#POS species3 species1 effect_s1 species2 effect_s2
7 C A non-synonymous T non-synonymous
15 G ...
written 1 day ago by
finswimmer ♦ 2.7k
Latest awards to finswimmer
Scholar
1 day ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
2 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
8 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
11 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
12 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
12 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
20 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
27 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
27 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
28 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
28 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
28 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
29 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Voter
7 weeks ago,
voted more than 100 times.
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
8 weeks ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1979 users visited in the last hour