Contents

1 Review and mapping of data for ChIP-seq analysis:

1.1 Review of bowtie and bowtie2 and mapping options

In order for the output to be a proper .sam file use the -S option to explicitly say that you want a .sam output. This is required for bowtie2, and ensures that the header is included in the .sam file which is important for downstream steps.

We will continue working with a ChIP-seq dataset from human cells. The factor that was IP’ed was ATF1 (SRR5331338). The fastq file for the experiment and control (Input SRR5331584) is here:
/home/FCAM/meds5420/data/ATF1/fastq/

You have already selected 10 million reads, aligned to a genome, converted to BED, sorted, converted to bedGraph, and visualized these data on the UCSC genome browser.

2 ChIP-seq analyses