User: alslonik

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alslonik140
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140
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Location:
Israel
Last seen:
1 day, 19 hours ago
Joined:
2 years, 12 months ago
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a*******@gmail.com

ARO, Voulkani research center

Posts by alslonik

<prev • 43 results • page 1 of 5 • next >
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Answer: A: Genome de novo annotation with Maker
... Hi, Here is the description of the repeat library construction and by pressing on the link of ProtExcluder you are getting the tar.gz with the script. There is also a link for manual. Good luck! Look for the link is in section: 4. Exclusion of gene fragments https://weatherby.genetics.utah.edu/MA ...
written 6 months ago by alslonik140
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Answer: A: How to make a rooted tree ultrametric
... I used function from here: [http://blog.phytools.org/2017/03/forceultrametric-method-for-ultrametric.html][1] [1]: http://blog.phytools.org/2017/03/forceultrametric-method-for-ultrametric.html for the same purpose - using cafe with the output of Orthofinder. Basically the code looked like thi ...
written 7 months ago by alslonik140
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Comment: C: Maker Gff3 file issues
... Hi, As people below answered me - you have to find the problem with the file, either using a script kindly provided below, or manually. I ended up opening the file with R tools and correcting it semi-manually. ...
written 7 months ago by alslonik140
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Answer: A: How to write a list of DNAStringsets as a FASTA file in R
... Just in case someone needed to save it as a list of fastas, like me, you can it with a for loop: for (i in names(myAAStringSetList)) { writeXStringSet(myAAStringSetList[[i]], filepath = paste0("path/to/your/directory/",i, ".fasta"), format = "fasta") } ...
written 10 months ago by alslonik140
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Answer: A: Idenity, e value or bitscore ?
... Just because I always bump into this one when I google for the article to cite for the cutoff for inferring homology between the two proteins **(important condition).** Here is the link: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820096/][1] And here is the citation: > The bit-score provides ...
written 12 months ago by alslonik140
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Comment: C: convert the gff3 file from ensembl into 'feature table' (Sequin format/.tbl file
... See [here,][1] maybe it helps. [1]: https://www.biostars.org/p/296960/ ...
written 16 months ago by alslonik140
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Filtering GFF annotations file
... Hi all. I am trying to filter my Maker annotation output in gff format. I filtered the total anotations based on AED score and other parameters (i.e similarity to known proteins of similar origin etc). I am using readGFF of rtracklayer library in R as a parser and a tool to manipulate the file. ...
R gff maker written 16 months ago by alslonik140
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Answer: A: Reviewing Maker annotation
... OK, I'll answer to myself, in case someone will need this in the future. [Here][1] is a nice pipeline of post-annotation. [1]: http://www.plantcell.org/content/suppl/2014/04/30/tpc.114.124297.DC1 ...
written 17 months ago by alslonik140
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Answer: A: List Of Genome Sequencing Centers/Institutes
... http://g-incpm.weizmann.ac.il/genomics/crown-institute-genomics , WIS, Rehovot, Israel ...
written 17 months ago by alslonik140
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Reviewing Maker annotation
... Hi all. I am working on an annotation a *denovo* plant genome with Maker pipeline. I am currently at a step of post-processing and there are some things that I am not sure about: I had 3 Maker iterations - an initial one and two consectutive with gene prediction using snap and augustus. I ran a rec ...
genome annotation maker written 17 months ago by alslonik140

Latest awards to alslonik

Popular Question 4 months ago, created a question with more than 1,000 views. For Filtering GFF annotations file
Popular Question 4 months ago, created a question with more than 1,000 views. For Genome de novo annotation with Maker
Popular Question 4 months ago, created a question with more than 1,000 views. For Maker Gff3 file issues
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Idenity, e value or bitscore ?
Popular Question 5 months ago, created a question with more than 1,000 views. For Maker Gff3 file issues
Popular Question 14 months ago, created a question with more than 1,000 views. For De novo plant genome assembly
Scholar 17 months ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed
Supporter 17 months ago, voted at least 25 times.
Student 18 months ago, asked a question with at least 3 up-votes. For Genome de novo annotation with Maker
Scholar 22 months ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed

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