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cbg-ethz / LongSom

LongSom tool for long-reads
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Barcode Subsetting #1

Open HarrisonWismer opened 2 months ago

HarrisonWismer commented 2 months ago

Hi! Excited to try out this tool.

I currently have cell barcodes with corresponding cell-type annotations but the cells/barcodes that were filtered out when I processed my data in Seurat are still present in my mapped BAM file. Should I use samtools to filter out unused barcodes or is this handled internally (ie. any barcodes lacking an annotation in the barcodes input file for LongSom is automatically removed or not considered). Thanks!

ArthurDondi commented 2 months ago

Hi! Thanks a lot for you interest in LongSom!

This is handled internally, with a report on the fraction of reads attributed to the barcodes you provide, the fraction for reads not having a barcode, and reads having a barcode that is not in the file.