Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing
) to extract a region around each gene of interest from the associated 10x BAM file. We then used grep to extract reads that were assigned to a given gene and those that were not.pipeline that takes in a pre-existing reference GTF file and RNA-seq BAM file and outputs a new GTF file that extends the old one using RNA-seq data.
We performed DE between the profiles of each guide and the profiles of the intergenic guide with Nebula v1.1.7 (ref.
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