bowtie2and 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:
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.