User: dtejadamartinez
dtejadamartinez • 20
- Reputation:
- 20
- Status:
- New User
- Location:
- Last seen:
- 5 months, 1 week ago
- Joined:
- 1 year, 9 months ago
- Email:
- d**************@gmail.com
Posts by dtejadamartinez
<prev
• 14 results •
page 1 of 2 •
next >
3
votes
1
answer
189
views
1
answer
... Hi,
I'm working with Omastandalone v. 2.3.0
I'm doing the all vs all comparisons with 25 species, they are almost done, however I got the next error recurrently, first just with one specie (then I deleted all the comparisons with that specie and they compute again right), but now they keep stoppi ...
written 7 months ago by
dtejadamartinez • 20
• updated
7 months ago by
adrian.altenhoff • 620
0
votes
1
answer
584
views
1
answers
... Thanks, then I will use biomart in R as you suggest.
I'm going to do positive selection analysis (dN/dS) ...
written 14 months ago by
dtejadamartinez • 20
0
votes
1
answer
584
views
1
answers
... Thanks,
If in Ensembl I select another format (not FASTA) it doesn't retrieve the option to download the cds ...
written 14 months ago by
dtejadamartinez • 20
3
votes
1
answer
584
views
1
answer
... Hi,
I download the orthologues fasta file (cds) for one gene in Ensembl, but the fasta file just have the ensembls ID and not the specie associated name.
How can I add the specie associated name to ensembls ID in a fasta file ?
(I need do that for hundred of genes)
Thanks, ...
written 14 months ago by
dtejadamartinez • 20
• updated
14 months ago by
finswimmer ♦ 12k
1
vote
1
answer
348
views
1
answer
... I have a .orthoxml outputs that are my results from Oma Standalone. To analyze the hierarchical orthologous groups (HOG) stored in OrthoXML files I need to use the Pyham application which requires the ETE toolkit.
I have a linux computer and I work using the command line, but I am new using python ...
written 16 months ago by
dtejadamartinez • 20
• updated
9 months ago by
Christophe Dessimoz • 570
0
votes
0
answers
315
views
0
answers
... I would be very grateful if you could answer me these question
** Can I run Oma Standalone by adding other genomes that are not found in OMA and run it with the all-all of the species that I previously downloaded?**
I ask it because I need to make the orthology comparisons with other multiple spe ...
written 16 months ago by
dtejadamartinez • 20
0
votes
1
answer
493
views
1
answers
... edited to add
The cluster use Sun Grid Engine, I'm still trying to run the data, including the Toy example, but this error always comes up:
Reading GO file...
Segmentation fault (core dumped)
Regards, ...
written 17 months ago by
dtejadamartinez • 20
0
votes
1
answer
493
views
1
answers
... edited to add
There is a moment where conversions seem ready but the file says: conversion.running
before that I run again OMA and I get the next error and the run die all.
line 18: ulimit: stack size: cannot modify limit: Operation not permitted
only_run_dbconv := true
Starting ...
written 17 months ago by
dtejadamartinez • 20
• updated
17 months ago by
genomax ♦ 71k
0
votes
1
answer
493
views
1
answer
... Hi,
Trying to run OMA on 2 different cluster. In one cluster, it ran up to 32%, in another one it is cut at the beginning and the conversions are not finished.
But I get the same following error in both cases:
1523613044.955060 - 1 - [pid 22699]: Computing Orcinus_orca vs Bos_taurus (Part 95 ...
written 17 months ago by
dtejadamartinez • 20
• updated
17 months ago by
adrian.altenhoff • 620
0
votes
1
answer
347
views
1
answer
... Hello,
I download 30 coding sequences genomes of different species from Ensembl or NCBI. In order to eliminate the transcripts and isoforms I used cd-hitest first and then I passed the files through TRANSDECODER.
In TRANSDECODER v.5.0.2 I did step 1 and 3, but the final file **fasta.transdecoder ...
written 18 months ago by
dtejadamartinez • 20
• updated
18 months ago by
lieven.sterck ♦ 5.8k
Latest awards to dtejadamartinez
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1680 users visited in the last hour