MACS to Signac

Question

[bioinformatics.girl]

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.

[ATpoint]

Please go through your previous questions and upvote helpful answers, mark the one that solved the issue as accepted. You opened an extensive number of questions and barely or did not do any upvoting st all. That's not how an open community works.

Answer 1

[LChart]

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.