Workflow Type: Galaxy

This workflow takes 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 compute 2 normalization for coverage: normalized by million reads and normalized by million reads in peaks. Will plot the number of reads for each fragment length.

Inputs

ID Name Description Type
PE fastq input #main/PE fastq input Should be a paired collection with ATAC-seq fastqs
  • array containing
    • File
bin_size #main/bin_size Bin size for normalized bigwig (usually 50bp is sufficient)
  • int
effective_genome_size #main/effective_genome_size Used by macs2:\nH. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000
  • int
reference_genome #main/reference_genome reference_genome
  • string

Steps

ID Name Description
4 Cutadapt (remove adapter + bad quality bases) toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.7+galaxy0
5 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy0
6 filter MAPQ30 concordant pairs and not mitochondrial pairs toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2
7 Get number of reads per chromosome toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5
8 remove PCR duplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
9 reads in chrM/MT for multiQC toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
10 convert BAM to BED to improve peak calling toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtobed/2.30.0+galaxy2
11 Compute fragment length histogram toolshed.g2.bx.psu.edu/repos/iuc/pe_histogram/pe_histogram/1.0.1
12 number of reads toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
13 Call Peak with MACS2 toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.2.9.1+galaxy0
14 compute 1/million reads toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
15 Bigwig from MACS2 (no norm) wig_to_bigWig
16 get summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_slopbed/2.30.0+galaxy1
17 summary of MACS2 toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/9.3+galaxy1
18 Convert 1/million reads to parameter param_value_from_file
19 Isolate each bigwig do normalize not average __APPLY_RULES__
20 Merge summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_mergebed/2.30.0
21 normalize by million reads toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0
22 Compute coverage on summits +/-500kb toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_coveragebed/2.30.0+galaxy1
23 number of reads in peaks toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
24 compute 1/million reads in peaks toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.0
25 Combine number of reads in peaks with total number of reads cat1
26 Convert 1/million reads in peaks to parameter param_value_from_file
27 reads in peaks multiQC toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
28 normalize by million reads in peaks Isolate each bigwig do normalize not average toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_average/deeptools_bigwig_average/3.5.4+galaxy0
29 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1

Outputs

ID Name Description Type
1kb around summits #main/1kb around summits n/a
  • File
BAM filtered rmDup #main/BAM filtered rmDup n/a
  • File
Coverage from MACS2 (bigwig) #main/Coverage from MACS2 (bigwig) n/a
  • File
MACS2 narrowPeak #main/MACS2 narrowPeak n/a
  • File
MACS2 report #main/MACS2 report n/a
  • File
MarkDuplicates metrics #main/MarkDuplicates metrics n/a
  • File
MultiQC on input dataset(s): Stats #main/MultiQC on input dataset(s): Stats n/a
  • File
MultiQC webpage #main/MultiQC webpage n/a
  • File
Nb of reads in summits +-500bp #main/Nb of reads in summits +-500bp n/a
  • File
bigwig_norm #main/bigwig_norm n/a
  • File
bigwig_norm2 #main/bigwig_norm2 n/a
  • File
histogram of fragment length #main/histogram of fragment length n/a
  • File
mapping stats #main/mapping stats n/a
  • File

Version History

v1.0 (latest) Created 29th Nov 2024 at 03:02 by WorkflowHub Bot

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help Creators and Submitter
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  • Lucille Delisle
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Lucille Delisle

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Created: 21st Oct 2022 at 03:01

Last updated: 17th Jan 2023 at 03:01

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