ecre_cds_analysis

Chip-based Library of E. coli Regulatory and Coding Elements

Testing

I am testing the github commit feature. Is my key right?

Prelude: Load RNASeq & DNASeq Data

In order to cut down on the number of bad reads that we are aligning and processing, we use what we know about the library sequences to throw away sequences that are too short.

First we use calc_rna_dna.R to get RNA and DNA read counts. We use a shell script that wraps Bowtie in order to grab the reads:

We throw away any reads that are shorter than the shortest RBS + CDS sequence, and then calculations to get the RNA/DNA ratio, counts, etc.