User: kissaj

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kissaj90
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Posts by kissaj

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Orientation in paired-end sequencing?
... I don't think that this is the question. Mate-Pair and Paired-End are COMPLETELY different. One (Mate-Pair) is a library construction method. The other (Paired-End) is a method of sequencing. The confusion arises from Pyro/454/Roche terminology wherein they used the term "mate-pair" to describe ...
written 21 months ago by kissaj90
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SILVA vs GreenGenes
... Hello, As of February 22nd (2017), is SILVA (https://www.arb-silva.de/) the preferred database for 16S analysis? I noticed that GreenGenes (http://greengenes.secondgenome.com/downloads) has not been updated since 2013. Thanks, Andor ...
18s 16s its metgenomics amplicon written 2.3 years ago by kissaj90
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Comment: C: Degenerate Nucleotide Sequences
... Actually, you can compile just by gcc -o prg prg.c ...
written 2.9 years ago by kissaj90
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Answer: A: Paired-end RNA Seq data: How to deal with unpaired data after trimmomatic
... Chuck it, it is broken. It shouldn't be very much (%-wise). If it is, you have a problem. ...
written 2.9 years ago by kissaj90
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PAML kappa and alpha
... Hello, What do the "kappa" and "alpha" parameters do in PAML? Thanks, Andor ...
kappa alpha paml rev written 3.1 years ago by kissaj90 • updated 3.1 years ago by natasha.sernova3.5k
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Answer: A: Multiple Sequence Alignment For Cdnas
... Hello, I align everything by amino acid first, using Clustal Omega (better than any other alignment program for AA;https://dx.doi.org/10.1038%2Fmsb.2011.75) (NB This is NOT ClustalW, nor ClustalX). Then I use CodonAlign 2.0 (http://wbiomed.curtin.edu.au/bioinf/CodonAlign.php) and the nucleotide ...
written 3.1 years ago by kissaj90
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Evolution/Selection on Amino Acids
... Hello, What's the "best" program to evaluate the positive selection of amino acids? I've used TreeSAAP before (which implements the PAML code base). But I was wondering if in the last five years there's been a better program developed? Thanks, Andor ...
codon treesaap selection paml written 3.2 years ago by kissaj90 • updated 3.2 years ago by genomax68k
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Comment: C: How to plot REVIGO r script
... Sorry - didn't understand the difference...(between comment and answer) ...
written 4.3 years ago by kissaj90
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Answer: A: How to plot REVIGO r script
... Hi,    Yeah, I don't think they'll help out.  I'll try, but, it's been my experience that the big drawback of free software is a complete lack of support after a tool has been developed and published.   My current "workaround" is to pull images from screen capture. Regards, Andor ...
written 4.3 years ago by kissaj90
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Answer: A: How to plot REVIGO r script
... more issues   Scale for 'size' is already present. Adding another scale for 'size', which will replace the existing scale. Scale for 'size' is already present. Adding another scale for 'size', which will replace the existing scale. Error: Use 'theme' instead. (Defunct; last used in version 0.9.1) ...
written 4.3 years ago by kissaj90

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For How to plot REVIGO r script

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