Difference between revisions of "ChIP-Seq Top2 in Yeast"
| Line 8: | Line 8: | ||
= Sample quality = | = 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 = | = Alignment to the S288C Reference = | ||
| − | == Bam quality == | + | == Bam quality, no filtering == |
=== First Experiment === | === First Experiment === | ||
| Line 31: | Line 32: | ||
= Alignment to the new W303 Reference = | = Alignment to the new W303 Reference = | ||
| − | == Bam quality == | + | == Bam quality, no filtering == |
=== First Experiment === | === First Experiment === | ||
| Line 46: | Line 47: | ||
* [http://stab.st-andrews.ac.uk/top2/bamquals2/ULS1_T2_IP_cad1_srtd_bamqc.html ULS1_T2_IP_E2] | * [http://stab.st-andrews.ac.uk/top2/bamquals2/ULS1_T2_IP_cad1_srtd_bamqc.html ULS1_T2_IP_E2] | ||
* [http://stab.st-andrews.ac.uk/top2/bamquals2/ULS1_T2_INP_cad1_srtd_bamqc.html ULS1_T2_INP_E2] | * [http://stab.st-andrews.ac.uk/top2/bamquals2/ULS1_T2_INP_cad1_srtd_bamqc.html ULS1_T2_INP_E2] | ||
| + | |||
| + | == 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 === | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULSIP_E1_cad1tro_srtd_bamqc.html ULS1_IP_E1] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULSINP_E1_cad1tro_srtd_bamqc.html ULS1_INP_E1] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WTIP_E1_cad1tro_srtd_bamqc.html WT_IP_E1] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WTINP_E1_cad1tro_srtd_bamqc.html WT_INP_E1] | ||
| + | |||
| + | === Second Experiment === | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_IP_cad1_srtd_bamqc.html ULS1_IP_E2] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_INP_cad1_srtd_bamqc.html ULS1_INP_E2] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WT_T2_IP_cad1_srtd_bamqc.html WT_T2_IP_E2] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/WT_T2_INP_cad1_srtd_bamqc.html WT_T2_INP_E2] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_T2_IP_cad1_srtd_bamqc.html ULS1_T2_IP_E2] | ||
| + | * [http://stab.st-andrews.ac.uk/top2/bamfiltquals0/ULS1_T2_INP_cad1_srtd_bamqc.html ULS1_T2_INP_E2] | ||
Revision as of 11:31, 8 August 2017
Contents
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>
