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JihedC / Snakemake_ATAC_2020

Repository for Jianhui's snakemake pipeline
MIT License
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Coverage over other bed files #4

Open JihedC opened 3 years ago

JihedC commented 3 years ago

For now the pipeline uses the gencode bedfile to measure chromatin accessibility around the gene body. We want to include other bedfiles, such as protein binding sites or repeat.

JihedC commented 3 years ago

We need to find a method to store the large bed file containing information about the transposable elements we are interested in.

JihedC commented 3 years ago

I have also noticed that the gencode gtf for the genes is not downloaded by the pipeline. I have added a rule for it, need to check if it works or not.