In a few months i'll be leaving my current lab, and hopefully entering a Ph.D program in Computational Biology. My co-workers produce a large amount of sequencing data, and I am currently the only wetlab scientist turned computational biologist in our lab so I thought it was important that I build a easy to use pipeline that anyone in the lab could use easily, at least until they find someone to replace me.
CIPHER is a easy to use low-level genomics processing pipeline for a variety of sequencing datasets. Currently it processes single-end and pair-ended ChIP-seq, RNA-seq, MNase-seq, GRO-seq, and DNase-seq data. CIPHER can be found HERE with a small README on how to use it as well as examples of the input files required.
The main reason for posting is to get some feedback on the tool and to fix some of the quirks. Hopefully with a couple of people trying to run their data through it, I can find and fix the bugs quickly.
Thanks in advance.
