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New protocols and scripts for ChIP

February 23, 2012

I just uploaded one of the first scripts I run when I get ChIP-seq data back.   It takes all the FASTQ files in a directory and maps them with Bowtie and eventually spits out a bedGraph file for visualization, as well as a lot of other sam, bam and bed files.  It’s all described in the readme.txt.  It is all located here: bowtie_wrapper_ChIP.

I also uploaded the native ChIP protocol I use.  It not original material but it is a good protocol nonetheless and can be found here: Native ChIP Protocol


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