ChIP-Seq Top2 peak-calling E2 - Revision history

Jw297: Protected "ChIP-Seq Top2 peak-calling E2" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

2018-06-04T09:19:56Z

Protected "ChIP-Seq Top2 peak-calling E2" ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))

Rf at 06:50, 21 July 2017

2017-07-21T06:50:39Z

Rf at 20:27, 20 July 2017

2017-07-20T20:27:54Z

Rf at 20:23, 20 July 2017

2017-07-20T20:23:42Z

Rf at 16:37, 17 July 2017

2017-07-17T16:37:46Z

Rf at 16:32, 17 July 2017

2017-07-17T16:32:29Z

Rf at 16:26, 17 July 2017

2017-07-17T16:26:50Z

Rf at 16:08, 17 July 2017

2017-07-17T16:08:09Z

Rf: Created page with "= Introduction = ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets. The generic pipeline One of the authors..."

2017-07-17T15:57:45Z

Created page with "= Introduction = ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets. The generic pipeline One of the authors..."

New page

= Introduction =

ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets.

The generic pipeline

One of the authors also has a tutorial which is formatted into wiki format (for easy copy-pasting) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].

= Exp 1: Browsing alignment to S288C reference genome =

[http://stab.st-andrews.ac.uk/S288 This] is the link to the genome browser.

* Tick items in the left hand panel to enable/disable visibility
* Hover mouse over loci position bar, it will change into a plus sign. Drag a region to zoom quickly into it.

= Exp1: Distances to Telomeres =

* Of the 166 wildtype peak regions, 22 overlaps with telomeres.
* Of the 124 ULS1 peak regions, 23 overlap with telomeres.

These cases are excluded from the distance distributions below.

== Wildtype ==

[[File:wt_teld0.png]]

== Uls1 ==

[[File:uls1_teld0.png]]

= Raw data description =

Mutant:
ULS1INP_S6_L001_R1_001.fastq.gz
ULS1INP_S6_L001_R2_001.fastq.gz
ULS1INP_S6_L002_R1_001.fastq.gz
ULS1INP_S6_L002_R2_001.fastq.gz
ULS1INP_S6_L003_R1_001.fastq.gz
ULS1INP_S6_L003_R2_001.fastq.gz
ULS1INP_S6_L004_R1_001.fastq.gz
ULS1INP_S6_L004_R2_001.fastq.gz
USL1IP_S7_L001_R1_001.fastq.gz
USL1IP_S7_L001_R2_001.fastq.gz
USL1IP_S7_L002_R1_001.fastq.gz
USL1IP_S7_L002_R2_001.fastq.gz
USL1IP_S7_L003_R1_001.fastq.gz
USL1IP_S7_L003_R2_001.fastq.gz
USL1IP_S7_L004_R1_001.fastq.gz
USL1IP_S7_L004_R2_001.fastq.gz

Wildtype:
WTINP_S4_L001_R1_001.fastq.gz
WTINP_S4_L001_R2_001.fastq.gz
WTINP_S4_L002_R1_001.fastq.gz
WTINP_S4_L002_R2_001.fastq.gz
WTINP_S4_L003_R1_001.fastq.gz
WTINP_S4_L003_R2_001.fastq.gz
WTINP_S4_L004_R1_001.fastq.gz
WTINP_S4_L004_R2_001.fastq.gz
WTIP_S5_L001_R1_001.fastq.gz
WTIP_S5_L001_R2_001.fastq.gz
WTIP_S5_L002_R1_001.fastq.gz
WTIP_S5_L002_R2_001.fastq.gz
WTIP_S5_L003_R1_001.fastq.gz
WTIP_S5_L003_R2_001.fastq.gz
WTIP_S5_L004_R1_001.fastq.gz
WTIP_S5_L004_R2_001.fastq.gz

= Raw dataset quality analysis =

Using FASTQC and them MultiQC.

Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].

= Adaptor-cutting and filtering procedure =

* First run was without any filtering or cutting.

= BAM file quality analysis =

Using BamQC.

== For the unfiltered reads ==

Results linked [http://stab.st-andrews.ac.uk/top2/bamqc.html here].

= Papers =

== Genome-Organizing Factors Top2 and Hmo1 Prevent Chromosome Fragility at Sites of S phase Transcription ==

link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16258

Abstract:
Specialized topoisomerases solve the topological constraints arising when replication forks encounter transcription. We have investigated the contribution of Top2 in S phase transcription. Specifically in S phase, Top2 binds intergenic regions close to transcribed genes. The Top2-bound loci exhibit low nucleosome density and accumulate gammaH2A when Top2 is defective. These intergenic loci associate with the HMG protein Hmo1 throughout the cell cycle and are refractory to the histone variant Htz1. In top2 mutants, Hmo1 is deleterious and accumulates at pericentromeric regions in G2/M. Our data indicate that Top2 is dispensable for transcription and that Hmo1 and Top2 bind in the proximity of genes transcribed in S phase suppressing chromosome fragility at the M-G1 transition. We propose that an Hmo1-dependent epigenetic signature together with Top2 mediate an S phase architectural pathway to preserve genome integrity.

== Topoisomerase II binds nucleosome-free DNA and acts redundantly with topoisomerase I to enhance recruitment of RNA Pol II in budding yeast ==

link: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22626

DNA topoisomerases are believed to promote transcription by removing excessive DNA supercoils produced during elongation. However, it is unclear how topoisomerases in eukaryotes are recruited and function in the transcription pathway in the context of nucleosomes. To address this problem we present high-resolution genome-wide maps of one of the major eukaryotic topoisomerases, Topoisomerase II (Top2) and nucleosomes in the budding yeast, Saccharomyces cerevisiae. Our data indicate that at promoters Top2 binds primarily to DNA that is nucleosome-free. However, although nucleosome loss enables Top2 occupancy, the opposite is not the case and the loss of Top2 has little effect on nucleosome density. We also find that Top2 is involved in transcription. Not only is Top2 enriched at highly transcribed genes, but Top2 is required redundantly with Top1 for optimal recruitment of RNA polymerase II at their promoters. These findings and the examination of candidate-activated genes suggest that nucleosome loss induced by nucleosome remodeling factors during gene activation enables Top2 binding, which in turn acts redundantly with Top1 to enhance recruitment of RNA polymerase II.

@@ Line 111: / Line 111: @@
 == Adaptor-cutting and filtering procedure ==
-cutadapt applied first (this is advised) and then trimmomatic is the following manner
+The program '''cutadapt''' was applied first (this is advised) and then '''trimmomatic''' in the following manner
 The integrated MultiQC report is as follows:
-* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html MultiQC].
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/multiqc_report.html MultiQC].
 The individual FastQC reports are as follows:
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R1_fastqc.html ULS1_INP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_INP_R1_cutad_q30l49_tro_fastqc.html ULS1_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R2_fastqc.html ULS1_INP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_INP_R2_cutad_q30l49_tro_fastqc.html ULS1_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R1_fastqc.html ULS1_IP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_IP_R1_cutad_q30l49_tro_fastqc.html ULS1_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R2_fastqc.html ULS1_IP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_IP_R2_cutad_q30l49_tro_fastqc.html ULS1_IP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_T2_INP_R1_cutad_q30l49_tro_fastqc.html ULS1_T2_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_T2_INP_R2_cutad_q30l49_tro_fastqc.html ULS1_T2_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_T2_IP_R1_cutad_q30l49_tro_fastqc.html ULS1_T2_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/ULS1_T2_IP_R2_cutad_q30l49_tro_fastqc.html ULS1_T2_IP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/WT_T2_INP_R1_cutad_q30l49_tro_fastqc.html WT_T2_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/WT_T2_INP_R2_cutad_q30l49_tro_fastqc.html WT_T2_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/WT_T2_IP_R1_cutad_q30l49_tro_fastqc.html WT_T2_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2]
+* [http://stab.st-andrews.ac.uk/top2/ffqc2/WT_T2_IP_R2_cutad_q30l49_tro_fastqc.html WT_T2_IP_R2]

@@ Line 92: / Line 92: @@
 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]
-* [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]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1]
-* [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]
 and then MultiQC to integrate the FASTQC files into one report
@@ Line 109: / Line 109: @@
 * [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html integrated quality report].
-= Adaptor-cutting and filtering procedure ==
+== Adaptor-cutting and filtering procedure ==
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R1_fastqc.html ULS1_INP_R1.fastq.gz]
+cutadapt applied first (this is advised) and then trimmomatic is the following manner
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R2_fastqc.html ULS1_INP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
+The integrated MultiQC report is as follows:
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html MultiQC].
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
+The individual FastQC reports are as follows:
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R1_fastqc.html ULS1_INP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_INP_R2_fastqc.html ULS1_INP_R2]
-* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R1_fastqc.html ULS1_IP_R1]
-* [http://stab.st-andrews.ac.uk/top2/ffqc0/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/ffqc0/ULS1_IP_R2_fastqc.html ULS1_IP_R2]
 and then MultiQC to integrate the FASTQC files into one report

← Older revision		Revision as of 20:23, 20 July 2017
Line 109:		Line 109:
	* [http://stab.st-andrews.ac.uk/top2/fqc1/multiqc_report.html integrated quality 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 ==
		+
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R1_fastqc.html ULS1_INP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_INP_R2_fastqc.html ULS1_INP_R2.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
		+	* [http://stab.st-andrews.ac.uk/top2/ffqc0/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].

@@ Line 87: / Line 87: @@
 (order not respected)
-= Raw dataset quality analysis =
+= Dataset quality analysis and filtering =
-Using FASTQC and then MultiQC to integrate the FASTQC files
+== Raw unfiltered data ==
 * [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]
@@ Line 103: / Line 105: @@
 * [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R2_fastqc.html WT_T2_IP_R2.fastq.gz]
-Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].
+and then MultiQC to integrate the FASTQC files into one report
 = Adaptor-cutting and filtering procedure =

@@ Line 90: / Line 90: @@
 Using FASTQC and then MultiQC to integrate the FASTQC files
-* [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]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1.fastqc.html ULS1_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R1_fastqc.html ULS1_IP_R1.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2.fastqc.html ULS1_IP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_IP_R2_fastqc.html ULS1_IP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1.fastqc.html ULS1_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R1_fastqc.html ULS1_T2_INP_R1.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2.fastqc.html ULS1_T2_INP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_INP_R2_fastqc.html ULS1_T2_INP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1.fastqc.html ULS1_T2_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R1_fastqc.html ULS1_T2_IP_R1.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2.fastqc.html ULS1_T2_IP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/ULS1_T2_IP_R2_fastqc.html ULS1_T2_IP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1.fastqc.html WT_T2_INP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R1_fastqc.html WT_T2_INP_R1.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2.fastqc.html WT_T2_INP_R2.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_INP_R2_fastqc.html WT_T2_INP_R2.fastq.gz]
-* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1.fastqc.html WT_T2_IP_R1.fastq.gz]
+* [http://stab.st-andrews.ac.uk/top2/fqc1/WT_T2_IP_R1_fastqc.html WT_T2_IP_R1.fastq.gz]
-* [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]
 Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].

← Older revision	Revision as of 09:19, 4 June 2018
(No difference)

@@ Line 67: / Line 67: @@
   ├── 2017-06-27-08-T2WTINP_S8_L004_R1_001.fastq.gz
   └── 2017-06-27-08-T2WTINP_S8_L004_R2_001.fastq.gz
 = Raw dataset quality analysis =
-Using FASTQC and them MultiQC.
+Using FASTQC and then MultiQC to integrate the FASTQC files
 Results linked [http://stab.st-andrews.ac.uk/top2/fastqc.html here].
@@ Line 76: / Line 107: @@
 = Adaptor-cutting and filtering procedure =
 = BAM file quality analysis =
@@ Line 83: / Line 113: @@
 == For the unfiltered reads ==

@@ Line 1: / Line 1: @@
 = Introduction =
-ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets.
+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) [http://stab.st-andrews.ac.uk/wiki/ChIP-seq_Tutorial here].
-= Exp 1: Browsing alignment to S288C reference genome =
+= Raw data =
-Wildtype:
+* ULS1 Immunoprecipitation files:
-  WTINP_S4_L001_R1_001.fastq.gz
+_06_27_07_Uls1IP-50925901
-  WTINP_S4_L001_R2_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L001_R1_001.fastq.gz
-  WTINP_S4_L002_R1_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L001_R2_001.fastq.gz
-  WTINP_S4_L002_R2_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L002_R1_001.fastq.gz
-  WTINP_S4_L003_R1_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L002_R2_001.fastq.gz
-  WTINP_S4_L003_R2_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L003_R1_001.fastq.gz
-  WTINP_S4_L004_R1_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L003_R2_001.fastq.gz
-  WTINP_S4_L004_R2_001.fastq.gz
+ ├── 2017-06-27-07-Uls1IP_S7_L004_R1_001.fastq.gz
-  WTIP_S5_L001_R1_001.fastq.gz
+ └── 2017-06-27-07-Uls1IP_S7_L004_R2_001.fastq.gz
-  WTIP_S5_L001_R2_001.fastq.gz
+* ULS1 Input files
-  WTIP_S5_L002_R1_001.fastq.gz
+_06_27_06_Uls1INP-50917952
-  WTIP_S5_L002_R2_001.fastq.gz
+ ├── 2017-06-27-06-Uls1INP_S6_L001_R1_001.fastq.gz
-  WTIP_S5_L003_R1_001.fastq.gz
+ ├── 2017-06-27-06-Uls1INP_S6_L001_R2_001.fastq.gz
-  WTIP_S5_L003_R2_001.fastq.gz
+ ├── 2017-06-27-06-Uls1INP_S6_L002_R1_001.fastq.gz
-  WTIP_S5_L004_R1_001.fastq.gz
+ ├── 2017-06-27-06-Uls1INP_S6_L002_R2_001.fastq.gz
-  WTIP_S5_L004_R2_001.fastq.gz
+ ├── 2017-06-27-06-Uls1INP_S6_L003_R1_001.fastq.gz
 = Raw dataset quality analysis =