atacseq/main

This workflow take as input a collection of paired fastq. It will remove bad quality and adapters with cutadapt. Map with Bowtie2 end-to-end. Will remove reads on MT and unconcordant pairs and pairs with mapping quality below 30 and PCR duplicates. Will compute the pile-up on 5' +- 100bp. Will call peaks and count the number of reads falling in the 1kb region centered on the summit. Will plot the number of reads for each fragment length.

Inputs

ID	Name	Description	Type
PE fastq input	PE fastq input	Should be a paired collection with ATAC-seq fastqs	File[]
effective_genome_size	effective_genome_size	Used by macs2:\nH. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000	int
reference_genome	reference_genome	reference_genome	string

Steps

ID	Name	Description
3	Cutadapt (remove adapter + bad quality bases)	toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0
4	Bowtie2 map on reference	toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1
5	filter MAPQ30 concordant pairs and not mitochondrial pairs	toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.1+galaxy0
6	Get number of reads per chromosome	toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4
7	remove PCR duplicates	toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.3
8	reads in chrM/MT for multiQC	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
9	convert BAM to BED to improve peak calling	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2
10	Compute fragment length histogram	toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1
11	number of reads	toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
12	Call Peak with MACS2	toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.7.1+galaxy0
13	get summits +/-500kb	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1
14	summary of MACS2	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
15	Bigwig from MACS2	wig_to_bigWig
16	Merge summits +/-500kb	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0
17	Compute coverage on summits +/-500kb	toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0
18	number of reads in peaks	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
19	Combine number of reads in peaks with total number of reads	cat1
20	reads in peaks multiQC	toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
21	MultiQC	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0

Outputs

ID	Name	Description	Type
mapping stats	mapping stats	n/a	File
MarkDuplicates metrics	MarkDuplicates metrics	n/a	File
BAM filtered rmDup	BAM filtered rmDup	n/a	File
histogram of fragment length	histogram of fragment length	n/a	File
MACS2 narrowPeak	MACS2 narrowPeak	n/a	File
MACS2 report	MACS2 report	n/a	File
Coverage from MACS2 (bigwig)	Coverage from MACS2 (bigwig)	n/a	File
1kb around summits	1kb around summits	n/a	File
Nb of reads in summits +-500bp	Nb of reads in summits +-500bp	n/a	File
MultiQC on input dataset(s): Stats	MultiQC on input dataset(s): Stats	n/a	File
MultiQC webpage	MultiQC webpage	n/a	File

atacseq/main
Version 1

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 23rd Nov 2022 at 10:41 by Finn Bacall

Creator

Submitter

atacseq/main Version 1

Inputs

Steps

Outputs

Version History

Version 1 (earliest) Created 23rd Nov 2022 at 10:41 by Finn Bacall

Creator

Submitter

Related items

atacseq/main
Version 1