ChIP-Seq Top2 peak-calling

Introduction

ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of of pairs each, for a total of 16 pairs of paired-end datasets.

Raw data description

Mutant:

ULS1INP_S6_L001_R1_001.fastq.gz
ULS1INP_S6_L001_R2_001.fastq.gz
ULS1INP_S6_L002_R1_001.fastq.gz
ULS1INP_S6_L002_R2_001.fastq.gz
ULS1INP_S6_L003_R1_001.fastq.gz
ULS1INP_S6_L003_R2_001.fastq.gz
ULS1INP_S6_L004_R1_001.fastq.gz
ULS1INP_S6_L004_R2_001.fastq.gz
USL1IP_S7_L001_R1_001.fastq.gz
USL1IP_S7_L001_R2_001.fastq.gz
USL1IP_S7_L002_R1_001.fastq.gz
USL1IP_S7_L002_R2_001.fastq.gz
USL1IP_S7_L003_R1_001.fastq.gz
USL1IP_S7_L003_R2_001.fastq.gz
USL1IP_S7_L004_R1_001.fastq.gz
USL1IP_S7_L004_R2_001.fastq.gz

Wildtype:

WTINP_S4_L001_R1_001.fastq.gz
WTINP_S4_L001_R2_001.fastq.gz
WTINP_S4_L002_R1_001.fastq.gz
WTINP_S4_L002_R2_001.fastq.gz
WTINP_S4_L003_R1_001.fastq.gz
WTINP_S4_L003_R2_001.fastq.gz
WTINP_S4_L004_R1_001.fastq.gz
WTINP_S4_L004_R2_001.fastq.gz
WTIP_S5_L001_R1_001.fastq.gz
WTIP_S5_L001_R2_001.fastq.gz
WTIP_S5_L002_R1_001.fastq.gz
WTIP_S5_L002_R2_001.fastq.gz
WTIP_S5_L003_R1_001.fastq.gz
WTIP_S5_L003_R2_001.fastq.gz
WTIP_S5_L004_R1_001.fastq.gz
WTIP_S5_L004_R2_001.fastq.gz

Raw dataset quality analysis

Using FASTQC and them MultiQC.

Results linked here.