Moderator: finswimmer
finswimmer ♦ 7.7k
- Reputation:
- 7,730
- Status:
- Trusted
- Location:
- Germany
- Last seen:
- 3 hours ago
- Joined:
- 1 year, 9 months ago
- Email:
- f***********@gmail.com
Posts by finswimmer
<prev
• 1,125 results •
page 1 of 113 •
next >
0
votes
0
answers
93
views
0
answers
... Could you please post the complete header of the original vcf file and the first few variants?
Thanks.
fin swimmer ...
written 5 hours ago by
finswimmer ♦ 7.7k
0
votes
1
answer
67
views
1
answers
Answer:
A: I16 Info Tag
... Hello https://www.biostars.org/u/50213/ ,
the output you are talking about, is the output of `bcftools mpileup`. And this is just the half way down the road to your variants. In this step `bcftools` collects metrics about each covered position on which `bcftools call` will decide if it should have ...
written 5 hours ago by
finswimmer ♦ 7.7k
0
votes
0
answers
119
views
0
answers
... - Can you index and align against `` only?
- Can you index and align against `` only?
- What's the output of `grep "chrV" -A 5 -B 5 `? ...
written 5 hours ago by
finswimmer ♦ 7.7k
0
votes
0
answers
77
views
0
answers
... Hello,
you have to make sure that the `bam` files are coordinate sorted before doing variant calling. At least the first sample isn't.
fin swimmer ...
written 1 day ago by
finswimmer ♦ 7.7k
0
votes
0
answers
77
views
0
answers
... How did you produce your bam file? Please show us the exact command used. ...
written 2 days ago by
finswimmer ♦ 7.7k
0
votes
0
answers
77
views
0
answers
... Hello and welcome to biostars https://www.biostars.org/u/50889/ ,
Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time.
Thank you.
Are you sure that you will have any variants in your `aligned.bam`?
> When I look at calls.b ...
written 2 days ago by
finswimmer ♦ 7.7k
0
votes
0
answers
93
views
0
answers
... > But since the file I am using is not a standard VCF file, I am not getting the desired output.
Could you please tell us, what makes your vcf a non standard vcf file?
fin swimmer ...
written 2 days ago by
finswimmer ♦ 7.7k
0
votes
0
answers
119
views
0
answers
... Could you please try to reindex `fusion38-10k.fa`. But this time without any parameters.
For -a bwtsw` you used I see a warning in the manual about it:
Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
`-a div' do not work not for long genomes.
Without sett ...
written 2 days ago by
finswimmer ♦ 7.7k
1
vote
0
answers
119
views
0
answers
... Let's check if the line ending terminators are correct.
$ file
: ASCII text
If the output is `: ASCII text, with CRLF line terminators` you should install `dos2unix` and run `dos2unix `.
fin swimmer ...
written 3 days ago by
finswimmer ♦ 7.7k
0
votes
0
answers
75
views
0
answers
... I guess it must be :
a.intersect(b, '-wb')
Take care of the quotation marks, otherwise python interpret `wb` as a variable.
fin swimmer ...
written 3 days ago by
finswimmer ♦ 7.7k
Latest awards to finswimmer
Librarian
4 days ago,
created a post with more than 10 bookmarks.
For Creating workflows with snakemake and conda
Teacher
4 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
5 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
5 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Teacher
5 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
5 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Popular Question
6 days ago,
created a question with more than 1,000 views.
For Creating workflows with snakemake and conda
Teacher
8 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Prophet
10 days ago,
created a post with more than 20 followers.
For Creating workflows with snakemake and conda
Scholar
11 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
15 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
18 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
20 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
23 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Appreciated
23 days ago,
created a post with more than 5 votes.
For A: Ensembl: Genes versus Transcripts
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Teacher
23 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
23 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Teacher
24 days ago,
created an answer with at least 3 up-votes.
For A: How to merge multiple bam files into single bam file
Scholar
24 days ago,
created an answer that has been accepted.
For A: How to merge multiple bam files into single bam file
Scholar
24 days 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: 999 users visited in the last hour