Add new ChIP-Seq WF that handles replicates and controls #581
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Hi, |
That's what I thought, too, even though I borrowed a lot from your WFs (like the entire backbone of the analysis, and the averaging across replicates), so if you want to, I can add you as a WF author. You may want to have a look at using fastp instead of cutadapt, which makes it possible to have optional adapter sequences and the updated samtools view step I'm using. Those could be integrated easily into your WF I guess. |
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Yes, I also think it would be beneficial to use fastp instead of cutadapt in all my workflows. |
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@wm75 it seems there is no 'Calculate numeric parameter value' tool on .org. |
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Funny, it's an iuc tool: https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param |
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Please add it here: https://github.com/galaxyproject/usegalaxy-tools |
| "owner": "bgruening", | ||
| "tool_shed": "toolshed.g2.bx.psu.edu" | ||
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| "tool_state": "{\"advancedOpt\": {\"showAdvancedOpt\": \"yes\", \"__current_case__\": 1, \"binSize\": \"50\", \"sortRegions\": \"keep\", \"sortUsing\": \"mean\", \"averageTypeBins\": \"mean\", \"missingDataAsZero\": true, \"skipZeros\": true, \"minThreshold\": null, \"maxThreshold\": null, \"scale\": null, \"metagene\": false, \"transcriptID\": \"transcript\", \"exonID\": \"exon\", \"transcript_id_designator\": \"transcript_id\", \"blackListFileName\": {\"__class__\": \"RuntimeValue\"}}, \"custom_sample_labels_conditional\": {\"custom_labels_select\": \"No\", \"__current_case__\": 0}, \"mode\": {\"mode_select\": \"reference-point\", \"__current_case__\": 1, \"referencePoint\": \"center\", \"nanAfterEnd\": false, \"beforeRegionStartLength\": \"3000\", \"afterRegionStartLength\": \"3000\"}, \"multibigwig_conditional\": {\"orderMatters\": \"No\", \"__current_case__\": 0, \"bigwigfiles\": {\"__class__\": \"ConnectedValue\"}}, \"output\": {\"showOutputSettings\": \"no\", \"__current_case__\": 0}, \"regionsFiles\": [{\"__index__\": 0, \"regionsFile\": {\"__class__\": \"ConnectedValue\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", |
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So the beforeRegionStartLength and the afterRegionStartLength here should not be hard-coded.
Initially I thought I could come up with a way to estimate them from the MACS2 peak region widths, but maybe we should just turn them into a WF param for now.
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Should we start with the hardcoded region length for tomorrow ?
workflows/epigenetics/chipseq-pe-with-replicates-controls/test-data/test_sample_sheet.tsv
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Not quite ready yet, but time to bring online.
@lldelisle another variation of the theme :-)
Essentially, an automated version of the steps in https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html#formation-of-the-super-structures-on-the-inactive-x