User: Pasta

gravatar for Pasta
Pasta1.3k
Reputation:
1,310
Status:
New User
Location:
Switzerland
Last seen:
5 years, 8 months ago
Joined:
8 years ago
Email:
p********@yahoo.com

Posts by Pasta

<prev • 105 results • page 1 of 11 • next >
0
votes
3
answers
3.9k
views
3
answers
Comment: C: Validation Of De Novo Rna-Seq Assembly
... Thank you for the link, I will have a look. ...
written 6.3 years ago by Pasta1.3k
10
votes
3
answers
3.9k
views
6 follow
3
answers
Validation Of De Novo Rna-Seq Assembly
... Hi, I recently performed the de novo assembly of plant RNA-seq data using Velvet/Oases with the multiple k-mer approach (merging of several sub-assemblies). The assembled transcripts were annotated and filtered for redundancy using CD-HIT EST. However, I still have a lot of different isoforms and ...
velvet rna-seq written 6.3 years ago by Pasta1.3k • updated 6.2 years ago by Wrf210
1
vote
2
answers
27k
views
2
answers
Comment: C: Fastq Quality Control Shootout
... Very good and straightforward tuto ! There is also SolexaQA for trimming: http://solexaqa.sourceforge.net/ ...
written 6.4 years ago by Pasta1.3k
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Oases "Confidence" - What Does It Mean ?
... Thank you for your suggestion ;) ...
written 6.4 years ago by Pasta1.3k
2
votes
1
answer
2.1k
views
1
answer
Oases "Confidence" - What Does It Mean ?
... Hi, Does anyone know what the confidence values exactly mean in the transcripts.fa file produced by Oases ? The documentation is very vague about it .... I found a bit of information on the Net (see below), but it doesn't make sense since I have values of 0, 1 or >1 The confidence scores assi ...
velvet rna-seq written 6.4 years ago by Pasta1.3k • updated 6.4 years ago by Istvan Albert ♦♦ 80k
8
votes
2
answers
2.8k
views
2
answers
What'S Your Pipeline For Gene Prediction On Prokaryotic Contigs ?
... Hi, There a few tools available to predict genes on bacterial genomes such as Glimmer, Prodigal and GeneMarkS. I tried them but they always make divergent predictions, so I was wondering if you are using some kind of pipeline to make a consensus gene prediction? More generally, what do you use for ...
gene prediction contigs written 7.2 years ago by Pasta1.3k • updated 7.2 years ago by Lee Katz2.9k
0
votes
1
answer
5.8k
views
1
answers
Comment: C: Running Glimmer: Training On Closely Related Species Sequences
... Thank you for this comprehensive answer Neil ! ...
written 7.2 years ago by Pasta1.3k
7
votes
1
answer
5.8k
views
1
answer
Running Glimmer: Training On Closely Related Species Sequences
... Hi, I got several contigs obtained from the sequencing of a bacterial strain. I would like to make ORF prediction using GLIMMER and perform the training on the genes of a closely related species. The problem is that I cannot figure out how to do that. I read the documentation but I still very confu ...
gene orf written 7.2 years ago by Pasta1.3k • updated 7.2 years ago by Neilfws48k
1
vote
3
answers
2.5k
views
3
answers
Answer: A: Blast Database Sequences Length
... If you are talking about the blast on the NCBI website, well you can you [slen] in the Entrez Query box. Check this link: Entrez Query If you are using a local Blast DB, then just make a DB with sequences of the good length. ...
written 7.2 years ago by Pasta1.3k
0
votes
3
answers
5.9k
views
3
answers
Comment: C: Convert Bam To Fastq With Pe & Se Reads
... Question edited with more details ...
written 7.2 years ago by Pasta1.3k

Latest awards to Pasta

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2114 users visited in the last hour