mbiokyle29

Keybase proof

I hereby claim:

• I am mbiokyle29 on github.
• I am kmse (https://keybase.io/kmse) on keybase.
• I have a public key ASApAma5p4cXFPrIjM9ELirD2g4eOPr4cGAPwPdL2fkG_go

To claim this, I am signing this object:

mbiokyle29

$ git clone git@github.com:mbiokyle29/perlpipe.git
$ cd perlpipe/perl

# Run Bowtie2 pipeline - With Directory of reads requires bowtie map build in the standard location 
$ bowtie/Bowtie2Pipe.pl -d read_directory/ -m map_base_name

# Run MOSAiCS pipeline
$ mosaics/MosaicsPipe.pl --dir working_dir --chip chip.sam --input input.sam

# Run Bowtie2-->MOSAiCS pipeline

mbiokyle29

$ git clone git@github.com:mbiokyle29/easy-variant.git
$ cd easy-variant/

# Normal Run
$ EasyVariant.pl --reference reference.fasta --sam experiment.sam

# Specify minimum depth and output vcf file
$ EasyVariant.pl --reference reference.fasta --sam experiment.sam --depth 20 --vcf 1

# Only call in a certain range

mbiokyle29

use Mosaics;
my $mos = Mosaics->new(out_loc => "./");

# Load chip and input data
$mos->chip_file('myChip.sam');
$mos->input_file('myInput.sam');

# Create bin-level data
$mos->make_chip_bin();
$mos->make_input_bin();

mbiokyle29

$ git clone git@github.com:mbiokyle29/MosaicsPerl.git
$ cd MosaicsPerl
$ sudo apt-get install libstatistics-r-perl