User: alslonik

gravatar for alslonik
alslonik110
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110
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Location:
Israel
Last seen:
2 weeks, 2 days ago
Joined:
2 years, 2 months ago
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a*******@gmail.com

ARO, Voulkani research center

Posts by alslonik

<prev • 40 results • page 1 of 4 • next >
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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 24 days ago by alslonik110
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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 10 weeks ago by alslonik110
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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 7 months ago by alslonik110
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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 7 months ago by alslonik110
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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 7 months ago by alslonik110
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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 7 months ago by alslonik110
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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 7 months ago by alslonik110
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Comment: C: Maker Gff3 file issues
... Hi, an update. Your script throws me a list of awful errors and no output: error: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: OBO File Format Error - Cannot find tag format-version and/ default-namespace . These are required header. STACK: Error::thro ...
written 8 months ago by alslonik110
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Comment: C: Gff3 file issues
... WOW. Thanks, Juke-34 I am going to try it. Al least I am not the only one!!! And I ran Maker with open MPI too... Thank you very much! ...
written 8 months ago by alslonik110
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Comment: C: Gff3 file issues
... Not sure that I understand... Yes, I did: ` gff3_merge -d logfile` I did not do any filtering while merging. ...
written 8 months ago by alslonik110

Latest awards to alslonik

Popular Question 4 months ago, created a question with more than 1,000 views. For De novo plant genome assembly
Scholar 7 months ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed
Supporter 7 months ago, voted at least 25 times.
Student 8 months ago, asked a question with at least 3 up-votes. For Genome de novo annotation with Maker
Scholar 13 months ago, created an answer that has been accepted. For A: Falcon - Estimation of free disc space needed

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