User: konstantinkul

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Posts by konstantinkul

<prev • 28 results • page 1 of 3 • next >
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Comment: C: Interproscan GO terms results expalnation
... Ok, I got it! Thanks a lot! ...
written 12 weeks ago by konstantinkul50
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Interproscan GO terms results explanation
... Hi all, I am new in InterPro scan as well as in genome annotation. I need to classify genes by GO terms to obtain a general table "GO Terms Classification Count Results" Could you please explain me one thing. When I run Interproscan with '-goterms' option it generated for me such output where seve ...
genome gene written 12 weeks ago by konstantinkul50 • updated 12 weeks ago by Michael Dondrup43k
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Comment: C: Pangenome Analysis using Roary tool
... Open file gene_presence_absence.csv in Excel and select all rows where 'No. isolates' equal to a number of analyzed genomes (strains). These genes will be core genes. ...
written 6 months ago by konstantinkul50
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Answer: A: Pangenome Analysis using Roary tool
... Install Roary and Prokka Go to path with fasta genomes > cd path/to/fastas/ Annotate fasta genomes with Prokka > for i in *.fa; do prokka $i --addgenes --locustag ${i%.*} --force --cpus 32; done Collect all GFF files from each genome folder to tm folder > mkdir t ...
written 6 months ago by konstantinkul50
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Answer: A: Phylogenetic tree for viruses
... Make MSA with mafft (http://mafft.cbrc.jp/alignment/server/) Find the best substitution model with MEGA Create phylogenetic tree using ML (maximum likelihood) methods with model defined in MEGA ...
written 6 months ago by konstantinkul50
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GenePrimp error: Illegal division by zero at BPlite.pm line 283, <$__ANONIO__> line 400764.
... Hello, Did anybody has the error while the GenePrimp (http://www.nature.com/nmeth/journal/v7/n6/full/nmeth.1457.html) parsing the Blastp output at the first stage of analysis. I have the same issue by analysis both the gbk file from ncbi and the gbk file produced by Prokka. I also tested the differ ...
software error gene genome written 8 months ago by konstantinkul50
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Comment: C: Genome coverage against normalized average depth
... Thank you for your reply. I have similar doubts about "theoretical" line. Let me explain my pipeline 1. I create coverage column for each position of ref genome `$ bedtools coverage -abam some.bam -b fasta.tab -d > cov.txt` extrat last column `cut -f 6 cov.txt > genome_depth` 2. In R `tab ...
written 11 months ago by konstantinkul50
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Genome coverage against normalized average depth
... Hello! Does anybody dealt with this type of graph "A plot of genome coverage against normalized average depth" http://prntscr.com/df9wmc. I really need it for optimization of procedures of WGS. I was trying to figure it out how to generate it, but I couldn't. The description in methods section was ...
R next-gen written 11 months ago by konstantinkul50 • updated 11 months ago by Brian Bushnell14k
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Comment: C: Parse figtree file with Python
... Thank you for suggestion! I'll try it! ...
written 21 months ago by konstantinkul50
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Parse figtree file with Python
... Hello, everyone! Does anybody has or know a python library\clasess\functions to parse files of figtree format file? I need to rename a bunch of tip labels. Thank you in advance!   ...
python figtree written 21 months ago by konstantinkul50 • updated 21 months ago by moranr220

Latest awards to konstantinkul

Popular Question 11 weeks ago, created a question with more than 1,000 views. For Convert fasta alignment to Vector NTI *.apr format
Popular Question 7 months ago, created a question with more than 1,000 views. For Pipeline For Amplicons Analysis
Popular Question 8 months ago, created a question with more than 1,000 views. For Pipeline For Amplicons Analysis
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