Table 1.

File formats used in ChIP-seq analysis.

File Type	Brief Description	Use in Analysis
FASTQ	Illumina sequencing file from experimental run	Raw ChIP-seq Data
FASTQC	Illumina quality control file for each Illumina sequencing run	Evaluating ChIP-seq Sequencing Data
SAM	Alignment file from Bowtie2 or BWA	Aligned ChIP-seq File
BAM	Binary SAM file	Aligned ChIP-seq File
wiggle (WIG)	File containing results of enumerating read hits at each base location	Visualization File
ELAND	Another alignment file format, used as input in MOSAiCS	For Peak Calling