Workflow Type: Galaxy

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+galaxy1
4 Bowtie2 map on reference toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.0+galaxy0
5 filter MAPQ30 concordant pairs and not mitochondrial pairs toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1
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+galaxy1

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

Version History

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

Updated to v1.0


Frozen v1.0 584746c

v0.17 Created 7th Oct 2024 at 16:32 by WorkflowHub Bot

Updated to v0.17


Frozen v0.17 292f448

v0.13 Created 7th Oct 2024 at 16:32 by WorkflowHub Bot

Updated to v0.13


Frozen v0.13 9ae67f2

v0.12 Created 7th Oct 2024 at 16:32 by WorkflowHub Bot

Updated to v0.12


Frozen v0.12 e05c5dc

v0.11 Created 7th Oct 2024 at 16:32 by WorkflowHub Bot

Updated to v0.11


Frozen v0.11 ce0395d

v0.10 Created 7th Oct 2024 at 16:32 by WorkflowHub Bot

Updated to v0.10


Frozen v0.10 3486b90

v0.16 Created 16th Jul 2024 at 03:02 by WorkflowHub Bot

Updated to v0.16


Frozen v0.16 baa8cf2

v0.15 Created 30th May 2024 at 11:35 by WorkflowHub Bot

Updated to v0.15


Frozen v0.15 32277c8

v0.14 Created 30th Apr 2024 at 03:02 by WorkflowHub Bot

Updated to v0.14


Frozen v0.14 b2f4734

v0.9 Created 24th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.9


Frozen v0.9 0559adb

v0.8 Created 20th Oct 2023 at 03:02 by WorkflowHub Bot

Updated to v0.8


Frozen v0.8 0c23e66

v0.7 Created 18th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.7


Frozen v0.7 b4e63b2

v0.6 Created 4th Oct 2023 at 03:01 by WorkflowHub Bot

Updated to v0.6


Frozen v0.6 9c9bc6f

v0.5.1 Created 26th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.5.1


Frozen v0.5.1 f81a8a2

v0.5 Created 1st Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 711274a

v0.4 Created 17th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 a465610

v0.3 Created 14th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 5f2a283

v0.2 Created 30th Nov 2022 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 e36373a

v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 1071145
help Creators and Submitter
Creator
  • Lucille Delisle
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Lucille Delisle

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Views: 7809   Downloads: 2188   Runs: 0

Created: 21st Oct 2022 at 03:01

Last updated: 17th Jan 2023 at 03:01

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