atacseq/main
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Tests 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 |
|
| effective_genome_size | effective_genome_size | Used by macs2:\nH. sapiens: 2700000000, M. musculus: 1870000000, D. melanogaster: 120000000, C. elegans: 90000000 |
|
| reference_genome | reference_genome | reference_genome |
|
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 |
|
| MarkDuplicates metrics | MarkDuplicates metrics | n/a |
|
| BAM filtered rmDup | BAM filtered rmDup | n/a |
|
| histogram of fragment length | histogram of fragment length | n/a |
|
| MACS2 narrowPeak | MACS2 narrowPeak | n/a |
|
| MACS2 report | MACS2 report | n/a |
|
| Coverage from MACS2 (bigwig) | Coverage from MACS2 (bigwig) | n/a |
|
| 1kb around summits | 1kb around summits | n/a |
|
| Nb of reads in summits +-500bp | Nb of reads in summits +-500bp | n/a |
|
| MultiQC on input dataset(s): Stats | MultiQC on input dataset(s): Stats | n/a |
|
| MultiQC webpage | MultiQC webpage | n/a |
|
Version History
v0.1 (earliest) Created 21st Oct 2022 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.11071145
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Views: 7454 Downloads: 2062 Runs: 0
Created: 21st Oct 2022 at 03:01
Last updated: 17th Jan 2023 at 03:01
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