User: agatorano

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agatorano40
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5 years, 5 months ago
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Posts by agatorano

<prev • 31 results • page 1 of 4 • next >
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Synteny Alignment To Phylogenetic Tree Using Mauve
... Hi, I want to obtain a tree from synteny alignment of various genomes. I have been using mauve (which I believe is based on local co-linear blocks or something rather, which sounds like synteny) and can output alignment files (such as xmfa) or potentially output a "guide tree" file in newick format. ...
alignment written 5.4 years ago by agatorano40 • updated 5.4 years ago by Biostar ♦♦ 20
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Comment: C: What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exom
... This is extremely interesting ...
written 5.5 years ago by agatorano40
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Comment: C: What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exom
... This is really helpful in the long term but even they admit to not knowing the parameters to use and why. ...
written 5.5 years ago by agatorano40
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What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exome
... Hello I am unsure how best to use BWA on two files containing haplotypes of an exome. There are three BWA types. I assume I am to be using the MEM algorithm but I am unsure what many of my options should be. For example what should my gap costs be? match? Are these things well established? what are ...
exome bwa written 5.5 years ago by agatorano40 • updated 2.8 years ago by Biostar ♦♦ 20
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Comment: C: Trouble Installing Blat Executables
... Thank you my machtype was empty. I have it set in my .bashrc file but it seems to only be in my environmental variables when it I export from the command line. Do I need to do this everytime? ...
written 5.6 years ago by agatorano40
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Comment: C: Trouble Installing Blat Executables
... Do you know where that may be? ...
written 5.6 years ago by agatorano40
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Trouble Installing Blat Executables
... I am getting this error when I run the make command on an executable. gcc -O -g -Wall -Wno-unused-variable -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_ -DUSE_SSL -DCOLOR32 -Wall -Wno-unused-variable -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../. ...
blat written 5.6 years ago by agatorano40 • updated 2.0 years ago by brianlee0
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(Closed) Trouble Installing Pirs On Mac Os X
... I have been having trouble installing the the program pIRS on my os x machine it says that its dependencies are BOOST and ZLIB I have installed both but this is still my error global.h:5: error: ‘boost’ is not a namespace-name global.h:5: error: expected namespace-name before ‘;’ token simulate_I ...
simulation mutation written 5.7 years ago by agatorano40 • updated 5.7 years ago by SES8.1k
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Comment: C: Contig Incompatibility For Depth Of Coverage Calculations Using Gatk
... SN:1 SN:2 SN:3 SN:4 SN:5 SN:6 SN:7 SN:8 SN:9 SN:10 SN:11 SN:12 SN:13 SN:14 SN:15 SN:16 SN:17 SN:18 SN:19 SN:20 SN:21 SN:22 SN:X SN:Y SN:MT SN:GL000207.1 SN:GL000226.1 SN:GL000229.1 SN:GL000231.1 SN:GL000210.1 SN:GL000239.1 SN:GL000235.1 SN:GL000201.1 SN:GL000247.1 SN:GL000245.1 SN:GL000197.1 SN:GL00 ...
written 5.8 years ago by agatorano40
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Comment: C: Contig Incompatibility For Depth Of Coverage Calculations Using Gatk
... Doing exactly that I get this output: @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @SQ @ ...
written 5.8 years ago by agatorano40

Latest awards to agatorano

Popular Question 5.8 years ago, created a question with more than 1,000 views. For Contig Incompatibility For Depth Of Coverage Calculations Using Gatk
Popular Question 6.0 years ago, created a question with more than 1,000 views. For Help With Multiple Whole Genome Alignment. Aligning Over 400 Whole Genomes

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