User: Picasa
Picasa • 480
- Reputation:
- 480
- Status:
- Trusted
- Location:
- Last seen:
- 3 hours ago
- Joined:
- 3 years, 9 months ago
- Email:
- p*********@gmail.com
Posts by Picasa
<prev
• 280 results •
page 1 of 28 •
next >
0
votes
1
answer
39
views
1
answer
... Hello,
I am trying to use SnpEff but I got a non model organism. I am trying now to build the database but my annotation is a Maker GFF format, and I got some issues
Anybody have experience with converting the maker GFF format to an other compatible one ) (ex: to GTF)
Thanks for your help. ...
written 5 days ago by
Picasa • 480
• updated
5 days ago by
prince26121991 • 60
1
vote
0
answers
73
views
0
answers
... So basically I had wgs data that I used to call variants (SNPs and indels) -> at the end .vcf file.
I have a reference genome fasta file and want to create an alternative genome fasta file (with SNPs and indels) -> This is easy.
But the difficulty is that I want to extract transcripts (so I ...
written 25 days ago by
Picasa • 480
0
votes
0
answers
73
views
0
answers
... Yes exactly, sorry for not being clear.
It's easy to integrate the alternative SNPs (haplotype 2) because it doesn't shift the coordinates of my transcripts (in the GTF), but for indels... I don't have any solutions. ...
written 26 days ago by
Picasa • 480
1
vote
0
answers
73
views
0
answers
... Hi,
I am studying allele specific expression and I am stuck on the step to get 2 transcripts (one from haplotype 1 and one from haplotype 2).
To get genes/transcripts from a GTF I use `cufflink gffreads`: this is not a problem.
Now I want to make version 2 (ie. haplotype 2, or alternative) of the ...
written 26 days ago by
Picasa • 480
0
votes
0
answers
110
views
0
answers
... Thanks for your link. Do you have experience with ASE study ? ...
written 7 weeks ago by
Picasa • 480
1
vote
0
answers
110
views
0
answers
... Hi all,
I am looking for your help about tools/pipeline for allele specific expression analysis. From various papers, I have come up with this pipeline:
1) Call variant with GATK using WGS samples
2) Create 2 transcriptomes using these variants and my annotation: so I have one transcriptome for ...
written 7 weeks ago by
Picasa • 480
0
votes
1
answer
152
views
1
answers
... Thanks I will take a look ...
written 8 weeks ago by
Picasa • 480
3
votes
1
answer
152
views
1
answer
... Hello,
I have old illumina genomes that I would like to improve with a scaffolding step.
For scaffolding I have long reads (pacbio or nanopore depending on species).
Do you have any softwares recommendation to do that ?
Thank you. ...
written 8 weeks ago by
Picasa • 480
• updated
8 weeks ago by
lieven.sterck ♦ 6.4k
0
votes
1
answer
714
views
1
answers
... Hi,
> For de novo I would suggest 30-40X, whereby the longest reads are the
> most important.
Do you have a source for this ? thanks. ...
written 3 months ago by
Picasa • 480
0
votes
2
answers
240
views
2
answers
Comment:
C: Location of centromere
... Thanks for the papers ! , I will take a look. ...
written 4 months ago by
Picasa • 480
Latest awards to Picasa
Popular Question
4 weeks ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For FASTA output in blast ?
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Full header in blastn out6 format ??
Popular Question
3 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For database for fungus ?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
4 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
5 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
6 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Sequence and assemble polyploid genome ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For database for fungus ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Tool for de novo assembly evaluation ??
Popular Question
7 months ago,
created a question with more than 1,000 views.
For database for fungus ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
7 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For database for fungus ?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For mate pair trimming ?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1034 users visited in the last hour