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You can skip this step The important thing is to understand what information is being provided by the file here: it's some metadata that can be used to compute the percentage of reads in peaks. There are other ways do to that without the file, but it's not essential to look at this value. |
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I'm analysing a multimome 10x dataset (snRNA + snATAC) I found in NCBI https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294559. However, they have not given the per_barcode_metrics.csv file, which is what is used for the peak_region_fragments metric, which is requied for the QC step:
seurat_obj$pct_reads_in_peaks <- seurat_obj$peak_region_fragments / seurat_obj$passed_filters * 100
All I have are the fragments files and the .h5 files (GeX + peaks).
Is there a way I can calculate these values by myself?
Can I skip this QC step? How important is it? And if I do skip it, will I ever not need it downstream?
Thanks in advance.
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