kkapuria3

Keybase proof

I hereby claim:

• I am kkapuria3 on github.
• I am kkapuria3 (https://keybase.io/kkapuria3) on keybase.
• I have a public key ASAAJ6Uwp8k3H65ktNpjm9HA07IFuQMQVhXiK0V5ll3Z-Ao

To claim this, I am signing this object:

kkapuria3

bwa mem -t 8 genome.fa reads.fastq | samtools sort -@ 8 -o output.bam 

kkapuria3

cpu=$(grep -c ^processor /proc/cpuinfo)

kkapuria3

##  If you run pip install awscli from cygwin, it may install awscli in Window's Anaconda Python installation, instead of in Cygwin's Python (which is what you want). Then, when you run aws configure, you will get an error that the aws executable can't be found. The solution is to try the following from a cygwin shell:

pip uninstall awscli
wget rawgit.com/transcode-open/apt-cyg/master/apt-cyg
install apt-cyg /bin
apt-cyg install python
wget https://bootstrap.pypa.io/get-pip.py
python get-pip.py
pip install awscli

kkapuria3

import paramiko
k = paramiko.RSAKey.from_private_key_file("/Users/whatever/Downloads/mykey.pem")
c = paramiko.SSHClient()
c.set_missing_host_key_policy(paramiko.AutoAddPolicy())
print "connecting"
c.connect( hostname = "www.acme.com", username = "ubuntu", pkey = k )
print "connected"
commands = [ "/home/ubuntu/firstscript.sh", "/home/ubuntu/secondscript.sh" ]
for command in commands:
	print "Executing {}".format( command )

kkapuria3

1    1       249250621                                                                                                                                 
2    1       243199373                                                                                                                                 
3    1       198022430                                                                                                                                 
4    1       191154276                                                                                                                                 
5    1       180915260                                                                                                                                 
6    1       171115067                                                                                                                                 
7    1       159138663                                                                                          

kkapuria3

Differential expression analysis with edgeR

This is a tutorial I have presented for the class Genomics and Systems Biology at the University of Chicago. In this course the students learn about study design, normalization, and statistical testing for genomic studies. This is meant to introduce them to how these ideas are implemented in practice. The specific example is a differential expression analysis with edgeR starting with a table of counts and ending with a list of differentially expressed genes.

Past versions:

• Tuesday, April 26, 2016

kkapuria3

$ aws --region=us-east-1e ec2 describe-spot-price-history --instance-types c4.4xlarge --start-time=$(date +%s) --product-descriptions="Linux/UNIX" --query 'SpotPriceHistory[*].{az:AvailabilityZone, price:SpotPrice}'

## Result

[
    {
        "price": "0.024900", 
        "az": "us-east-1e"
    }
]