Difference between revisions of "ChIP-Seq Top2 peak-calling E2"
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(order not respected) | (order not respected) | ||
| − | = | + | = Dataset quality analysis and filtering = |
| − | Using FASTQC | + | == Raw unfiltered data == |
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| + | 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.fastq.gz] | ||
* [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.fastq.gz] | ||
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* [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.fastq.gz] | ||
| − | + | 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]. | ||
= Adaptor-cutting and filtering procedure = | = Adaptor-cutting and filtering procedure = | ||
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Revision as of 16:37, 17 July 2017
Contents
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:
- 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
and then MultiQC to integrate the FASTQC files into one report
