User: pablo61991

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pablo6199110
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2 months, 2 weeks ago
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Posts by pablo61991

<prev • 17 results • page 1 of 2 • next >
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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 5 days ago by pablo6199110
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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 6 days ago by pablo6199110
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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 6 days ago by pablo6199110
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Comment: C: Gene pathway analysis
... Perfect, I'll apply this approach. As soon as I have done it successfully, I'll comeback to vote this answer. Thank you. ...
written 20 days ago by pablo6199110
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Comment: C: Gene pathway analysis
... Sorry, I'll try to explain myself better. I don't know if it's possible to annotate my transcriptome vs *Danio rerio* database (mRNA or protein), then perform the GO analysis and finally, in order to obtain the list of genes which I need to perform the DGE analysis in DESeq2 (I follow the: kallist ...
written 20 days ago by pablo6199110
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Comment: C: Gene pathway analysis
... Thank you for your anwser EagleEye, yes, I have read this topic but I was interested in an alternative to could use several species during my annotation instead of one. However, what I have found here (you and others) and in other forums/web resources make me think there isn't a good alternative to ...
written 20 days ago by pablo6199110
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Comment: C: Gene pathway analysis
... Yes, as EagleEyes said, I'm also very interested in the end of the question. If it is solved maybe I can follow the same route. I'm also blocked in a similar issue. I have a transcriptome of a mollusk specie but I can't do the GO analysis. I didn't find a proper solution to my needs. I'm working wi ...
written 20 days ago by pablo6199110
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Comment: C: DESeq2 + de novo assembly
... Yep, I know about Sleuth but for any reason my supervisor has some kind of preference for DESeq2. I think is the eternal problem of "that is the software which I saw more times cited in the bibliography" even if in this particular case other software fits better to that DGE. I'm interested in that ...
written 4 weeks ago by pablo6199110
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Comment: C: retrieve normalised count data from DESeq2
... Oh, thank you I missed the default parameter. ...
written 4 weeks ago by pablo6199110
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Comment: C: retrieve normalised count data from DESeq2
... And to obtain the count matrix before the normalization just change `normalized = TRUE` for `normalized = FALSE`? ...
written 4 weeks ago by pablo6199110

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