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JihedC / Snakemake_ATAC_2020

Repository for Jianhui's snakemake pipeline
MIT License
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Add annotation of the peaks with Homer #6

Closed JihedC closed 3 years ago

JihedC commented 3 years ago

Homer can be used to annotate the peaks detected by ATAC-seq. This will give us information about the genomic feature associated with the peak.

Information about peak annotation: http://homer.ucsd.edu/homer/ngs/annotation.html

Homer can be installed with Conda: https://anaconda.org/bioconda/homer

WJH58 commented 3 years ago

@JihedC Rule homer has been added to the pipeline on dev branch.

JihedC commented 3 years ago

Ok! Can you provide an example of the output?

WJH58 commented 3 years ago

@JihedC The outputs of homer are stored in: /exports/humgen/Jianhui/pipeline_test/Snakemake_ATAC_2020/ATAC-seq_pipeline/results/annotation. There are KO1_annotate_homer.txt, KO2_annotate_homer.txt, WT1_annotate_homer.txt, WT2_annotate_homer.txt.

Here attached one example: KO1_annotate_homer.txt

Screenshot 2021-02-17 at 09 12 05
JihedC commented 3 years ago

I am not sure it work, there are no annotation of your peaks

JihedC commented 3 years ago

If it still does not work may be you can just give instructions to the user on how to perform the annotation.

WJH58 commented 3 years ago

@JihedC I've tried my best but I can't make Snakemake install mm10 when running the pipeline. Can we delete this rule? How do I give instruction? Can I state it in README?

WJH58 commented 3 years ago

@JihedC Maybe do you know someone who is good at Perl?

WJH58 commented 3 years ago

@JihedC I added a "Annotate peaks using Homer.md" file on dev branch.

JihedC commented 3 years ago

perfect!