atacseq/main
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Tests 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 |
|
| bin_size | #main/bin_size | Bin size for normalized bigwig (usually 50bp is sufficient) |
|
| effective_genome_size | #main/effective_genome_size | Used by macs2:\nH. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000 |
|
| reference_genome | #main/reference_genome | reference_genome |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Cutadapt (remove adapter + bad quality bases) | toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.6+galaxy1 |
| 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+galaxy1 |
| 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+galaxy0 |
| 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+galaxy0 |
| 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+galaxy0 |
| 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+galaxy0 |
| 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 |
|
| BAM filtered rmDup | #main/BAM filtered rmDup | n/a |
|
| Coverage from MACS2 (bigwig) | #main/Coverage from MACS2 (bigwig) | n/a |
|
| MACS2 narrowPeak | #main/MACS2 narrowPeak | n/a |
|
| MACS2 report | #main/MACS2 report | n/a |
|
| MarkDuplicates metrics | #main/MarkDuplicates metrics | n/a |
|
| MultiQC on input dataset(s): Stats | #main/MultiQC on input dataset(s): Stats | n/a |
|
| MultiQC webpage | #main/MultiQC webpage | n/a |
|
| Nb of reads in summits +-500bp | #main/Nb of reads in summits +-500bp | n/a |
|
| bigwig_norm | #main/bigwig_norm | n/a |
|
| bigwig_norm2 | #main/bigwig_norm2 | n/a |
|
| histogram of fragment length | #main/histogram of fragment length | n/a |
|
| mapping stats | #main/mapping stats | n/a |
|
Version History
v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.11071145
Creators and Submitter
Views: 18373 Downloads: 16898 Runs: 3
Created: 21st Oct 2022 at 03:01
Last updated: 17th Jan 2023 at 03:01
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