User: pablo61991

gravatar for pablo61991
pablo6199130
Reputation:
30
Status:
New User
Location:
Last seen:
21 hours ago
Joined:
6 months, 1 week ago
Email:
p*********@gmail.com

Posts by pablo61991

<prev • 24 results • page 1 of 3 • next >
0
votes
1
answer
177
views
1
answers
Comment: C: primer desing for qPCR on de novo assembly output
... Thank you Kevin, I have more success using your tips ;) ...
written 12 days ago by pablo6199130
0
votes
1
answer
177
views
1
answers
Comment: C: primer desing for qPCR on de novo assembly output
... Sorry but is something wrong? I can see a lot of views but no answers or comments, there is something wrong in my statement? ...
written 9 weeks ago by pablo6199130
2
votes
1
answer
177
views
1
answer
primer desing for qPCR on de novo assembly output
... Hello community, I have searched in forums and google looking for help in primer design for confirmation assay by qPCR of de novo assembly transcripts. When I blast my transcripts, I have obtained different levels of identity against the blast hit and when I have to design my primers I don´t know i ...
rnaseq primer qpcr written 9 weeks ago by pablo6199130 • updated 6 weeks ago by Kevin Blighe3.3k
0
votes
1
answer
258
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... No we let the default config, I think it is something like 200 nt of min size. In my opinion your way to do it is fine, but my supervisor its paranoiac about lose biological relevant information, even when we finish the assembly with tha huge amount of high redundant data (and for sure, also a lot o ...
written 3 months ago by pablo6199130
0
votes
1
answer
258
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Thank you for the clarification, I have done the same. In our case we really need to reduce the redundancy of our transcriptome because we have obtained more than 1.000.000 transcripts and CD-hit est didn't help (reduce the dataset but we still had 900k transcripts) for that reason we don't check th ...
written 3 months ago by pablo6199130
0
votes
1
answer
258
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Just to point it out, (I think) he is the author of the tool ;) (congrats Mr. Gilbert). ...
written 3 months ago by pablo6199130
0
votes
1
answer
258
views
1
answers
Comment: C: EvidentialGene reduces redundancy of de novo transcriptome assembly?
... Hello crimsontabaq, I have some questions about how do you use that tool. I have looked for a way to send you a private message but I think that is not possible in this forum. As consequence I have to put my question here (sorry). How do you have applied the EG approach? do you have touched several ...
written 3 months ago by pablo6199130
1
vote
1
answer
312
views
1
answers
Comment: C: trying to use gnu parallel and blast
... Oh shame on me... I didn't try it on a subset of data and maybe it just show and output when the blast finished. I mean, I have run this command for 12 h to try to calculate the % of the transcriptome blasted and estimate how much time I need. However, my output was an empty file. That makes me go i ...
written 4 months ago by pablo6199130
1
vote
1
answer
312
views
1
answers
Answer: C: trying to use gnu parallel and blast
... I have read in this forum a topic discussing how blast use multiple-core resources with this option (link here): [https://www.biostars.org/p/63816/][1] In a short search maybe this don't make a big difference, but in a search against nr and using shared resources I need to optimize my search as mu ...
written 4 months ago by pablo6199130
4
votes
1
answer
312
views
6 follow
1
answer
trying to use gnu parallel and blast
... Dear Biostar community, I have problems to run a blastx against nr database. To optimize the process I have read some post which mentioned gnu parallel as a solution to optimize the use of multiple CPUs by ncbi-blast (local mode). Based on different post of this forum I have adapted my code until I ...
gnu parallel parallel blastx blast optimization written 4 months ago by pablo6199130

Latest awards to pablo61991

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: 743 users visited in the last hour