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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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GREAT Input #33

Closed JBreunig closed 5 years ago

JBreunig commented 5 years ago

Hi Rongxin,

What is the most facile way to generate BED files for passing to GREAT?

Thanks! J

r3fang commented 5 years ago

there is package in R call rGREAT (https://bioconductor.org/packages/release/bioc/html/rGREAT.html) it is the best way to run GREAT analysis

JBreunig commented 5 years ago

Sorry for not being more specific in the question above but what variable/object name (containing BED info) should be passed based on your 10X tutorial? (I did find the "target" bed file generated in the homer directory that I can manually pass but I'm wondering if there is an easier way...x.sp@??) Thanks again!