As the doctor gone rogue

February 20, 2014

A note on getting start with samtools on Mac OsX 10.8.5 Mountain Lion

Filed under: NGS — Tags: , , , , — hypotheses @ 9:50 pm

samtools is a handy tool for sequence alignment and mapping (http://samtools.sourceforge.net/

For more information, please refer to the original article here:

  • Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

To get it to work on mac, I’ve decided to compile it.

First, get the sourcecode from http://sourceforge.net/projects/samtools/files/samtools/

Then, decompress the files in ~/bin

Compile it as usual

./configure
make
make install

You might need to have administrative right to write to system folder as well.

Next, we'll need to add a path to ~/.bash_profile

Include this in ~/.bash_profile to point to SAMTOOLS_HOME

export SAMTOOLS_HOME=~/bin/samtools-0.1.19
export PATH=$SAMTOOLS_HOME:$PATH
export PATH=$SAMTOOLS_HOME/bcftools/:$PATH
export PATH=$SAMTOOLS_HOME/misc/:$PATH

Now, samtools should be ready for you to use.

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July 26, 2013

How to wget with proxy authentication?

Filed under: bash, NGS — Tags: , , , — hypotheses @ 2:25 am

Once again, I have a problem with proxy server authentication through my university network. Trying to install the new KGGSeq software to do next-generation sequencing data analysis.

As a quick fix, with cygwin, here is what I did.

1. Need to tell bash that  that we are using a proxy server

## Add these to ~/.bashrc for my bash start up shell


## Add these to ~/.bashrc for my bash start up shell

proxy="http://user:password@proxy-server.university:8080"
export http_proxy=$proxy

2. Need to tell wget what username and password to use with the proxy server.

As an example to download KGGSeq through cygwin, here’s what I did.

wget --proxy-user "bhoom" --proxy-password "bhoom_password"  http://statgenpro.psychiatry.hku.hk/limx/kggseq/download.php?file=kggseq.zip

Wget – ArchWiki.

I’m still not quite sure why they still use it. There seems to be several other enterprise authentication system, but all other systems are probably pricy? But does price justify all the other troubles we all have with slow connection for every website, problems running many bioinformatics software that cannot connect through proxy-server, etc?

June 16, 2013

Ion Torrent PGM vs PacBio vs MiSeq

Filed under: genetics, NGS — hypotheses @ 1:05 am

“It’s a lot cheaper to buy PGM compared to other sequencing platform. So, should we buy it?”

A common concern regarding this question is whether the sequencing quality is alright? This is one of the first concern Ion Torrent seems to have experience since they first launched their first sequencer.

Quail, et al took a look at three platform in their paper. Although they have only looked at microbial genome with variable GC/AT content. They showed that there still seems to be a problem with Ion Torrent PGM platform when they sequence Plasmodium genome. Moreover, the false positive rate of base calling from Ion Torrent platform is still higher.

This data may not be applicable to human genome sequencing, but it deserves a closer look in my opinion.

BMC Genomics | Full text | A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers.

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