reconstructing the analysis from the paper from eLife 2017

[yeroslaviz]

Hi,

I'm trying to understand how you analyze the data in the paper from 2017 in eLife journal, "An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites".

I have found the scripts on your github (as you can clearly see :-) ), but I'm not sure how to go through them.

I would appreciate a short explanation or a confirmation of my workflow.

I have a dataset of three samples in paired-end mode (six fastq files). The analyzed organism is Mouse.

I would first like to map the samples to the genome and than create the bed/bigwig files splitted by size ( ≤120 bp and ≥150 bp ).

Am I correct in first using py_bowtie_fastq_2_sam script, following by py_sam_2_avenormbg?

Is it enough to copy the files to my working directory and run them (of course, after I have the bowtie2 index of my organism)

thanks
Assa