View source for 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 [[http:stab.st-andrews.ac.uk/stab/top2/fastqc.html here]].

= Papers =