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

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* [http://stab.st-andrews.ac.uk/top2/bamfiltquals3/ULS1_T2_IP_srtd_filt3_bamqc.html ULS1_T2_IP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals3/ULS1_T2_IP_srtd_filt3_bamqc.html ULS1_T2_IP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals3/ULS1_T2_INP_srtd_filt3_bamqc.html ULS1_T2_INP_E2]
 
* [http://stab.st-andrews.ac.uk/top2/bamfiltquals3/ULS1_T2_INP_srtd_filt3_bamqc.html ULS1_T2_INP_E2]
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= MACS Peak categories and Signal =
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 +
It is not totally clear how MACS decides that a peak should be called. This is apparent when the signal appears to rise and fall, yet MACS does not call a peak.
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== Signal script ==
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The source for this is from teh MACS developer and is detailed [https://gist.github.com/taoliu/2469050 here].
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= Differential Peak-calling =
 
= Differential Peak-calling =

Revision as of 16:13, 9 October 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

MACS Peak categories and Signal

It is not totally clear how MACS decides that a peak should be called. This is apparent when the signal appears to rise and fall, yet MACS does not call a peak.

Signal script

The source for this is from teh MACS developer and is detailed here.


Differential Peak-calling

Macs2 incorporated differential peak calling somewhat later into its set of tools. The idea is to take two conditions and compare their peaks.

The pipeline to follow is probably Macs2's recommended one at Differential Binding Events