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

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  samtools view -b -F 1820 -q 48 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>
 
  samtools view -b -F 1820 -q 48 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>
 +
 +
=== First Experiment ===
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULSIP_E1_srtd_filt_bamqc.html ULS1_IP_E1]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULSINP_E1_srtd_filt_bamqc.html ULS1_INP_E1]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WTIP_E1_srtd_filt_bamqc.html WT_IP_E1]
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* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WTINP_E1_srtd_filt_bamqc.html WT_INP_E1]
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=== Second Experiment ===
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_IP_srtd_filt_bamqc.html ULS1_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_INP_srtd_filt_bamqc.html ULS1_INP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WT_T2_IP_srtd_filt_bamqc.html WT_T2_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WT_T2_INP_srtd_filt_bamqc.html WT_T2_INP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_T2_IP_srtd_filt_bamqc.html ULS1_T2_IP_E2]
 +
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_T2_INP_srtd_filt_bamqc.html ULS1_T2_INP_E2]
 +
 +
== Bam quality, 2nd filtering applied ==
 +
 +
This time bam files were filtered to MAPQ 28:
 +
 +
samtools view -b -F 1820 -q 28 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>
  
 
=== First Experiment ===
 
=== First Experiment ===

Revision as of 22:29, 8 August 2017

Introduction

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

Sample quality

In the above previous analyses, we undertook some Duplicate removel as this showed up to be an issue in the FastQC quality files.

However, the effect of this removal was very low. In any case, the MACS2 program takes care of duplicates so samples were only trimmed for adapters and quality.

Alignment to the S288C Reference

Bam quality, no filtering

First Experiment

Second Experiment

Alignment to the new W303 Reference

Bam quality, no filtering

First Experiment

Second Experiment

Bam quality, filtering applied

The bam files were filtered both for mapping quality and low integrity reads in the following manner: 

samtools view -b -F 1820 -q 48 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>

First Experiment

Second Experiment

Bam quality, 2nd filtering applied

This time bam files were filtered to MAPQ 28: 

samtools view -b -F 1820 -q 28 <INBAMFILE> -o ${OUTBAMFILE> -@ <NUMTHREADS>

First Experiment

Second Experiment

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