How I get fraction fragments in peak without metadata in sc ATAC-seq with Signac ? · Biostar

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How I get fraction fragments in peak without metadata in sc ATAC-seq with Signac ?

Hi everyone!

I am analyzing sc ATAC-seq data with Signal tool integrated with Seurat. I only have the peak matrix and the fragment file. The metadata from cellranger has not been provided to me. To perform the quality control step I filtered the samples by the nucleosomal signal, TSS enrichment score and blacklist ratio. However I want to annotate in the metadata the total number of fragments in peak and the fraction of fragments in peaks. I have tried the last one with the FRiP function but the results of this is very low ( the highest values in only 1.4%).

Does anyone know how I can get these metrics correctly without the metadata?

I also want to to ask what is the nCount_peak and nFeature_peak that appear by default in the atac metadata and how they differ.

Could it be that nFeature_peak is the count of fragments in peaks and I can get the percentage of fragment in peak from it?

Thank very much in advance and sorry for my English!

atac-seq seurat signac single-cell

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updated 2.7 years ago by Ram

• written 3.6 years ago by sarapascu98 •

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