User:Konrad U Foerstner/Tools and procedures

SNP calling

With Samtools

• Important. Base alignment quality (BAQ) is switched on per default and very (too) strict 5 Things to Know About SAMtools Mpileup

TSS prediction

• TSSi (untested)

Pathway visualization

• iPath2.0 (by Takuji!) - the modified and original maps can be downloaded as SVG (e.g. full metabolic map)
• KEGG Mapper (untested)

Trascription Terminator prediction

• TransTerm

Python

General useful libraries

• NumPy/SciPy
• panda
• statsmodels
• beautiful soup
• BioPython
• matplotlib
• ipython
• PyCogent

Misc

• Making matplotlib look like ggplot