User: mar.ark.parr

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mar.ark.parr40
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Posts by mar.ark.parr

<prev • 12 results • page 1 of 2 • next >
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Comment: C: KaKs_calculator doesn't work with sequences
... Thank you for this point! Yes, I currently it is not implemented. I found it can be done with http://translatorx.co.uk/ ...
written 7 months ago by mar.ark.parr40
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Comment: C: KaKs_calculator doesn't work with sequences
... Hi! The problem is found and its not in sequences. I filled the input files myself and didn't put "\n" at the end of the file. Ka/Ks Calculator needs it. @lieven.sterck Thanks for your answer! I have MSA of certain genes and take sequences from there pairwise. ...
written 7 months ago by mar.ark.parr40
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KaKs_calculator doesn't work with sequences
... Hi! Question about KaKs_Calculator2.0 I would like to calculate Ka/Ks for the sequences below. However, the calculator doesn't work with it. The tool doesn't write any error, however the output file is empty. Does anyone have any idea what is the problem? Kind regards, Marina sequences GTG ...
software error gene sequence written 7 months ago by mar.ark.parr40 • updated 7 months ago by RamRS26k
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Comment: C: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Thank you for the answer! ...
written 7 months ago by mar.ark.parr40
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Comment: C: Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Thanks a lot for the answer! ...
written 7 months ago by mar.ark.parr40
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Mapping NCBI Genome Accessions - NCBI Taxonomy IDs
... Hi all, I have list of NCBI genome accessions (SAMN02441064, NC_014374, NZ_ACYB00000000 ...) and would like to know taxonomic IDs of the species that they belong to. Is there a mapping file somewhere? Or how can I find their taxonomic IDs programmatically? Thanks in advance, Marina ...
genome ncbi taxonomy genbank written 7 months ago by mar.ark.parr40 • updated 7 months ago by genomax80k
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SciClone on WES data
... Hello everyone! I have recently installed SciClone (https://www.biostars.org/p/246374/) and now trying to apply it to WES data of two tumors. Firstly, I used VarScan2 to call somatic variants, then I separate output file on germline, somatic or LOH. I took somatic (as vaf data) and LOH (as regions ...
dnacopy varscan clonality wes sciclone written 2.9 years ago by mar.ark.parr40 • updated 18 months ago by aliz06110
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Answer: A: SciClone installation in R version 3.3.3
... For anyone who will struggle with this problem :) This is what finally helped me. Combining what guys here wrote me and advices of the colleagues from my lab: When devtools library has been already installed and "install_github("genome/bmm")" done: `sudo rm -r /tmp/*` `sudo apt-get install libx11 ...
written 3.0 years ago by mar.ark.parr40
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Comment: C: SciClone installation in R version 3.3.3
... Santosh, I apologize for late response and thank you very much again for your help! But unfortunately even if i install X11 by the way you said, SciClone still doesn't see. It still has the same error with rgl and X11... So as I understood the possible solution is to try another R version... Older o ...
written 3.0 years ago by mar.ark.parr40
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Comment: C: SciClone installation in R version 3.3.3
... Thank you very much! Really decided to keep manual installation as plan B :) ...
written 3.0 years ago by mar.ark.parr40

Latest awards to mar.ark.parr

Popular Question 2.9 years ago, created a question with more than 1,000 views. For SciClone installation in R version 3.3.3
Popular Question 2.9 years ago, created a question with more than 1,000 views. For SciClone on WES data

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