User: Anton Shekhov

gravatar for Anton Shekhov
Reputation:
60
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Location:
Germany/Jena/MPI ICE
Last seen:
3 years, 11 months ago
Joined:
4 years, 9 months ago
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s***********@gmail.com

Posts by Anton Shekhov

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Tophat2 with GTF annotation file made from blast results
... In the perfect world I would. However, there is no genome for this or even close related species. ...
written 4.0 years ago by Anton Shekhov60
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Comment: C: Tophat2 with GTF annotation file made from blast results
... yep, I guess I tried all the standard solutions there are in the internet. ...
written 4.0 years ago by Anton Shekhov60
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Comment: C: Tophat2 with GTF annotation file made from blast results
... Even though it won't fix this problem I am thinking to use STAR. ...
written 4.0 years ago by Anton Shekhov60
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Comment: C: Tophat2 with GTF annotation file made from blast results
... Bowtie2-build and bowtie worked perfectly before tophat2 step. It only did not work during tophat process. The names of the chromosomes are the same everywhere, I checked it several times. ...
written 4.0 years ago by Anton Shekhov60
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Tophat2 with GTF annotation file made from blast results
... Hi! The goal of my subproject is to find transcripts upregulated upon treatment in the larvae of Spodoptera littoralis. On the current step I have an assembly, and the tblastx results (assembly against the huge database from NCBI). In order to continue with annotation I transformed blast results in ...
tophat bowtie blast rna-seq written 4.0 years ago by Anton Shekhov60 • updated 4.0 years ago by EagleEye6.6k
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Comment: C: Reveal GO Biological Process using biomaRt
... Thanks! Did not realize that I omit all GO terms except the first one when connect two data frames. ...
written 4.5 years ago by Anton Shekhov60
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Comment: C: conditional loop does not work for plotting in R !!
... What do you mean by "plot only last one"? Does it produce only one graph for the whole for-loop? Or that without if it plots? ...
written 4.5 years ago by Anton Shekhov60
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Reveal GO Biological Process using biomaRt
... Hello dear community, I was wondering is it possible to get an access to the GO: Biological process for every gene name in transcriptome?  In more details: I have an Drosophila RNA-Seq data, which I analyzed by DESeq2. After that I wanted to cluster genes by their functions. For that I used biomaR ...
R biomart go rna-seq written 4.5 years ago by Anton Shekhov60 • updated 4.5 years ago by Emily_Ensembl21k
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Comment: C: if the DEseq package already installed?
... Probably the error in case-sensitivity of package name. You installed DESeq but searching for DEseq The another approach to check is it installed - is just to call any function from this package. The function you can find in vignette. The solution I first showed is for automatic checking mostly ...
written 4.8 years ago by Anton Shekhov60 • updated 7 months ago by RamRS27k
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Comment: C: if the DEseq package already installed?
... The answer to your question is here http://stackoverflow.com/questions/4090169/elegant-way-to-check-for-missing-packages-and-install-them And btw, you can install DESeq2, which contains all the functionality of the first version with extra features ...
written 4.8 years ago by Anton Shekhov60 • updated 7 months ago by RamRS27k

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