MACS to Signac
Hey guys--
Once MACS is completed running, how would I feed the peaks/bed file into Signac for each sample up to merging and finally clustering? I believe the vignette only demonstrates if one were to add *fragment files and I need the peaks file from MACS for a stronger signal.
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ATpoint
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bioinformatics.girl •
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bioinformatics.girl •
1 answer
If you have externally defined peaks, you can use
library(rtracklayer)
peaks = import('/path/to/peaks.bed')
FeatureMatrix(
fragments=CreateFragmentObject('/path/to/fragments.tsv'),
features=peaks
)
This will generate a peak quantification matrix, which you can push into a Seurat object for downstream analysis.
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