Difference between revisions of "ChIP-Seq Top2 peak-calling E2"

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Line 92: Line 92:
  
 
Using FASTQC to view quality aspects inidvidually:
 
Using FASTQC to view quality aspects inidvidually:
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_INP_R1_fastqc.html ULS1_INP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_INP_R1_fastqc.html ULS1_INP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_INP_R2_fastqc.html ULS1_INP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_INP_R2_fastqc.html ULS1_INP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2]
  
 
and then MultiQC to integrate the FASTQC files into one report
 
and then MultiQC to integrate the FASTQC files into one report
Line 109: Line 109:
 
* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html integrated quality report].
 
* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html integrated quality report].
  
−
= Adaptor-cutting and filtering procedure ==
+
== Adaptor-cutting and filtering procedure ==
  
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R1_fastqc.html ULS1_INP_R1.fastq.gz]
+
cutadapt applied first (this is advised) and then trimmomatic is the following manner
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R2_fastqc.html ULS1_INP_R2.fastq.gz]
+
 
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
+
The integrated MultiQC report is as follows:
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
+
 
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html MultiQC].
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
+
 
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
+
The individual FastQC reports are as follows:
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
+
 
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R1_fastqc.html ULS1_INP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R2_fastqc.html ULS1_INP_R2]
−
* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R1_fastqc.html ULS1_IP_R1]
−
* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2.fastq.gz]
+
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R2_fastqc.html ULS1_IP_R2]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1]
 +
* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2]
  
 
and then MultiQC to integrate the FASTQC files into one report
 
and then MultiQC to integrate the FASTQC files into one report
−
 
−
* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html integrated quality report].
 

Revision as of 20:27, 20 July 2017

Introduction

Experiment 2, or the second part of Top2 - ULS1 ChIP-Seq ipeak-calling

One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) here.

Raw data

  • ULS1 Immunoprecipitation files:
2017_06_27_07_Uls1IP-50925901
├── 2017-06-27-07-Uls1IP_S7_L001_R1_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L001_R2_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L002_R1_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L002_R2_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L003_R1_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L003_R2_001.fastq.gz
├── 2017-06-27-07-Uls1IP_S7_L004_R1_001.fastq.gz
└── 2017-06-27-07-Uls1IP_S7_L004_R2_001.fastq.gz
  • ULS1 Input files
2017_06_27_06_Uls1INP-50917952
├── 2017-06-27-06-Uls1INP_S6_L001_R1_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L001_R2_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L002_R1_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L002_R2_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L003_R1_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L003_R2_001.fastq.gz
├── 2017-06-27-06-Uls1INP_S6_L004_R1_001.fastq.gz
└── 2017-06-27-06-Uls1INP_S6_L004_R2_001.fastq.gz
  • Top2 Wildtype Immunoprecipitation files
2017_06_27_09_T2WTIP-50922924
├── 2017-06-27-09-T2WTIP_S9_L001_R1_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L001_R2_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L002_R1_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L002_R2_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L003_R1_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L003_R2_001.fastq.gz
├── 2017-06-27-09-T2WTIP_S9_L004_R1_001.fastq.gz
└── 2017-06-27-09-T2WTIP_S9_L004_R2_001.fastq.gz
  • Top2 Wildtype Input file
2017_06_27_10_T2Uls1INP-50926896
├── 2017-06-27-10-T2Uls1INP_S10_L001_R1_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L001_R2_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L002_R1_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L002_R2_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L003_R1_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L003_R2_001.fastq.gz
├── 2017-06-27-10-T2Uls1INP_S10_L004_R1_001.fastq.gz
└── 2017-06-27-10-T2Uls1INP_S10_L004_R2_001.fastq.gz
  • Top2 ULS1 Immunoprecipitation files:
2017_06_27_11_T2Uls1IP-50919923
   ├── 2017-06-27-11-T2Uls1IP_S11_L001_R1_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L001_R2_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L002_R1_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L002_R2_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L003_R1_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L003_R2_001.fastq.gz
   ├── 2017-06-27-11-T2Uls1IP_S11_L004_R1_001.fastq.gz
   └── 2017-06-27-11-T2Uls1IP_S11_L004_R2_001.fastq.g
  • Top2 ULS1 Input files
2017_06_27_08_T2WTINP-50917953
├── 2017-06-27-08-T2WTINP_S8_L001_R1_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L001_R2_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L002_R1_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L002_R2_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L003_R1_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L003_R2_001.fastq.gz
├── 2017-06-27-08-T2WTINP_S8_L004_R1_001.fastq.gz
└── 2017-06-27-08-T2WTINP_S8_L004_R2_001.fastq.gz

Concatenation

Splitting the rawdata into lanes is not really necessary for these experiments, so the above were concatenated to form: 

rawcatdata/
├── ULS1_INP_R1.fastq.gz
├── ULS1_INP_R2.fastq.gz
├── ULS1_IP_R1.fastq.gz
├── ULS1_IP_R2.fastq.gz
├── ULS1_T2_INP_R1.fastq.gz
├── ULS1_T2_INP_R2.fastq.gz
├── ULS1_T2_IP_R1.fastq.gz
├── ULS1_T2_IP_R2.fastq.gz
├── WT_T2_INP_R1.fastq.gz
├── WT_T2_INP_R2.fastq.gz
├── WT_T2_IP_R1.fastq.gz
└── WT_T2_IP_R2.fastq.gz

(order not respected)

Dataset quality analysis and filtering

Raw unfiltered data

Using FASTQC to view quality aspects inidvidually:

and then MultiQC to integrate the FASTQC files into one report

Adaptor-cutting and filtering procedure

cutadapt applied first (this is advised) and then trimmomatic is the following manner

The integrated MultiQC report is as follows:

The individual FastQC reports are as follows:

and then MultiQC to integrate the FASTQC files into one report

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