User: dtejadamartinez

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Posts by dtejadamartinez

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Comment: A: How can I add the specie associated name to ensembls ID in a fasta file (cds) ?
... 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 dtejadamartinez10
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Comment: A: How can I add the specie associated name to ensembls ID in a fasta file (cds) ?
... 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 dtejadamartinez10
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How can I add the specie associated name to ensembls ID in a fasta file (cds) ?
... 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, ...
ensembl written 5 months ago by dtejadamartinez10 • updated 5 months ago by finswimmer7.9k
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Pyham - pyham.taxonomy.Taxonomy object by constructing a ete3.Etree
... 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 ...
hogs orthoxml pyham written 6 months ago by dtejadamartinez10 • updated 5 days ago by Christophe Dessimoz500
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Export OMA all-all comparisons and add other species to run Oma Standalone
... 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 ...
oma browser oma standalone written 6 months ago by dtejadamartinez10
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Comment: C: Error ruining OMA "OneMachineParallelInfo"
... 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 dtejadamartinez10
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Comment: A: Error ruining OMA "OneMachineParallelInfo"
... 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 dtejadamartinez10 • updated 8 months ago by genomax59k
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Error ruining OMA "OneMachineParallelInfo"
... 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 ...
omastandalone oma written 8 months ago by dtejadamartinez10 • updated 7 months ago by adrian.altenhoff440
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TRANSDECODER v5.0.2 - nucleotide sequences with ambiguity characters S,R,W,K, Y
... 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 ...
transdecoder written 8 months ago by dtejadamartinez10 • updated 8 months ago by lieven.sterck3.3k
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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 dtejadamartinez10

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