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  - 01_Intro_chipseq_data_organization.md
  - 02_QC_FASTQC.md
  - 03_align_and_filtering.md
  - 04_peak_calling_macs.md
  - 05_combine_chipQC_and_metrics.md
  - 06_handling-replicates-bedtools.md
  - 07_handling-replicates-idr.md
  - 08_diffbind_differential_peaks.md
  - 10_data_visualization.md
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  - 12_annotation_functional_analysis.md
  - 12_functional_analysis.md
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  - OLD_QC_quality_metrics.md
  - QC_quality_metrics.md
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  - align_filter_automation.md
  - compare_callers_IGV.md
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sessionVI
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lessons

marypiper

Update 03_align_and_filtering.md

Oct 11, 2018

d7eff64 · Oct 11, 2018

History

Name	Name	Last commit message	Last commit date
parent directory ..
01_Intro_chipseq_data_organization.md	01_Intro_chipseq_data_organization.md	Update 01_Intro_chipseq_data_organization.md	Oct 3, 2018
02_QC_FASTQC.md	02_QC_FASTQC.md	Update 02_QC_FASTQC.md	Sep 26, 2018
03_align_and_filtering.md	03_align_and_filtering.md	Update 03_align_and_filtering.md	Oct 11, 2018
04_peak_calling_macs.md	04_peak_calling_macs.md	addding path to BAM since no automation	Oct 1, 2018
05_combine_chipQC_and_metrics.md	05_combine_chipQC_and_metrics.md	Update 05_combine_chipQC_and_metrics.md	Oct 3, 2018
06_handling-replicates-bedtools.md	06_handling-replicates-bedtools.md	removing image and a confusing line	Oct 2, 2018
07_handling-replicates-idr.md	07_handling-replicates-idr.md	Rename 09_handling-replicates-idr.md to 07_handling-replicates-idr.md	Oct 2, 2018
08_diffbind_differential_peaks.md	08_diffbind_differential_peaks.md	Update 08_diffbind_differential_peaks.md	Oct 4, 2018
10_data_visualization.md	10_data_visualization.md	Update 10_data_visualization.md	Oct 3, 2018
11_qualitative_assessment_IGV.md	11_qualitative_assessment_IGV.md	Update 11_qualitative_assessment_IGV.md	Oct 3, 2018
12_annotation_functional_analysis.md	12_annotation_functional_analysis.md	Update 12_annotation_functional_analysis.md	Oct 4, 2018
12_functional_analysis.md	12_functional_analysis.md	Update 12_functional_analysis.md	Oct 4, 2018
CC_metrics_extra.md	CC_metrics_extra.md	Update CC_metrics_extra.md	Oct 3, 2018
ChIPQC_quality_report_R.md	ChIPQC_quality_report_R.md	Rename 07_ChIPQC_quality_report_R.md to ChIPQC_quality_report_R.md	Oct 2, 2018
OLD_QC_quality_metrics.md	OLD_QC_quality_metrics.md	Rename 07_QC_quality_metrics.md to OLD_QC_quality_metrics.md	Oct 1, 2018
QC_quality_metrics.md	QC_quality_metrics.md	Rename 06_QC_quality_metrics.md to QC_quality_metrics.md	Oct 2, 2018
README.md	README.md	Update README.md	Jun 27, 2017
align_filter_automation.md	align_filter_automation.md	Rename 04_automation.md to align_filter_automation.md	Oct 1, 2018
compare_callers_IGV.md	compare_callers_IGV.md	pushing the new chipseq materials	Sep 26, 2018
integrating_rna-seq_and_chip-seq.md	integrating_rna-seq_and_chip-seq.md	Update integrating_rna-seq_and_chip-seq.md	Nov 7, 2017
orchestra_mounting.md	orchestra_mounting.md	Update orchestra_mounting.md	Jun 30, 2017
peak_calling_spp.md	peak_calling_spp.md	changing macs2 small details	Jun 11, 2017
qc_deeptools.md	qc_deeptools.md	pushing the new chipseq materials	Sep 26, 2018

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