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Commit d9e3b2b4 authored by Venkat Malladi's avatar Venkat Malladi
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Update documentation and use GTF file.

parent f6951a42
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1 merge request!67Resolve "Rename Plot profile to be consistent with naming"
Pipeline #6321 failed with stages
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...@@ -73,6 +73,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git ...@@ -73,6 +73,7 @@ $ git clone git@git.biohpc.swmed.edu:BICF/Astrocyte/chipseq_analysis.git
9. Annotate all peaks using ChipSeeker 9. Annotate all peaks using ChipSeeker
10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment) 10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
11. Use MEME-ChIP to find motifs in original peaks 11. Use MEME-ChIP to find motifs in original peaks
12. Plot enrichment of signal around TSS
See [FLOWCHART](docs/flowchart.pdf) See [FLOWCHART](docs/flowchart.pdf)
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...@@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste ...@@ -20,6 +20,7 @@ Report issues to the Bioinformatic Core Facility [BICF](mailto:BICF@UTSouthweste
9. Annotate all peaks using ChipSeeker 9. Annotate all peaks using ChipSeeker
10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment) 10. Calculate Differential Binding Activity with DiffBind (If more than 1 rep in more than 1 experiment)
11. Use MEME-ChIP to find motifs in original peaks 11. Use MEME-ChIP to find motifs in original peaks
12. Plot enrichment of signal around TSS
## Workflow Parameters ## Workflow Parameters
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...@@ -488,6 +488,7 @@ process plotProfile { ...@@ -488,6 +488,7 @@ process plotProfile {
output: output:
file '*.{png,gz}' into plotProfile file '*.{png,gz}' into plotProfile
file gtf from gtfFile
when: when:
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