Difference between revisions of "ChIP-Seq Top2 in Yeast"

From wiki
Jump to: navigation, search
Line 10: Line 10:
 
The MACS2 program takes care of duplicates so samples were only trimmed for adapters and quality.
 
The MACS2 program takes care of duplicates so samples were only trimmed for adapters and quality.
  
= Bam quality =
 
  
== First Experiment ==
+
= Alignment to the S288C Reference =
 +
 
 +
== Bam quality ==
 +
 
 +
=== First Experiment ===
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSIP_E1_cad1tro_srtd_bamqc.html ULS1_IP_E1]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSINP_E1_cad1tro_srtd_bamqc.html ULS1_INP_E1]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WTIP_E1_cad1tro_srtd_bamqc.html WT_IP_E1]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WTINP_E1_cad1tro_srtd_bamqc.html WT_INP_E1]
 +
 
 +
=== Second Experiment ===
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_IP_cad1_srtd_bamqc.html ULS1_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_INP_cad1_srtd_bamqc.html ULS1_INP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WT_T2_IP_cad1_srtd_bamqc.html WT_T2_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WT_T2_INP_cad1_srtd_bamqc.html WT_T2_INP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_T2_IP_cad1_srtd_bamqc.html ULS1_T2_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_T2_INP_cad1_srtd_bamqc.html ULS1_T2_INP_E2]
 +
 
 +
= Alignment to the new W303 Reference =
 +
 
 +
== Bam quality ==
 +
 
 +
=== First Experiment ===
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSIP_E1_cad1tro_srtd_bamqc.html ULS1_IP_E1]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSIP_E1_cad1tro_srtd_bamqc.html ULS1_IP_E1]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSINP_E1_cad1tro_srtd_bamqc.html ULS1_INP_E1]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULSINP_E1_cad1tro_srtd_bamqc.html ULS1_INP_E1]
Line 18: Line 39:
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WTINP_E1_cad1tro_srtd_bamqc.html WT_INP_E1]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/WTINP_E1_cad1tro_srtd_bamqc.html WT_INP_E1]
  
== Second Experiment ==
+
=== Second Experiment ===
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_IP_cad1_srtd_bamqc.html ULS1_IP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_IP_cad1_srtd_bamqc.html ULS1_IP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_INP_cad1_srtd_bamqc.html ULS1_INP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamquals0/ULS1_INP_cad1_srtd_bamqc.html ULS1_INP_E2]

Revision as of 14:40, 7 August 2017

Introduction

This wiki page combines the two sequencing experiments of ChIP-Seq on yeast samples udring June / July 2017.

Sample quality

The MACS2 program takes care of duplicates so samples were only trimmed for adapters and quality.


Alignment to the S288C Reference

Bam quality

First Experiment

Second Experiment

Alignment to the new W303 Reference

Bam quality

First Experiment

Second Experiment