User: dtejadamartinez
dtejadamartinez • 10
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Posts by dtejadamartinez
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... Thanks, then I will use biomart in R as you suggest.
I'm going to do positive selection analysis (dN/dS) ...
written 5 months ago by
dtejadamartinez • 10
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... Thanks,
If in Ensembl I select another format (not FASTA) it doesn't retrieve the option to download the cds ...
written 5 months ago by
dtejadamartinez • 10
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... 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 5 months ago by
dtejadamartinez • 10
• updated
5 months ago by
finswimmer ♦ 7.9k
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... 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 6 months ago by
dtejadamartinez • 10
• updated
5 days ago by
Christophe Dessimoz • 500
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... 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 6 months ago by
dtejadamartinez • 10
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... 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 7 months ago by
dtejadamartinez • 10
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... 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 8 months ago by
dtejadamartinez • 10
• updated
8 months ago by
genomax ♦ 59k
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... 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 8 months ago by
dtejadamartinez • 10
• updated
7 months ago by
adrian.altenhoff • 440
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... 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 8 months ago by
dtejadamartinez • 10
• updated
8 months ago by
lieven.sterck • 3.3k
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Answer:
A: start OMA run - file.log
... Hi, thanks for the answer.
I have all the sequences in nucleotides, and in the input I have InputDataType := 'DNA'; That's why I find it strange.
It only happens with the final files thrown by TRANSDECODER.
Cheers,
Daniela ...
written 8 months ago by
dtejadamartinez • 10
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