Hi,
I want to quantify separately exonic and intronic reads in my single-cell data. To do so, I have applied CellRanger to the same exact FASTQ files, with and without the --include-introns flag. I assumed that by subtracting the exonic counts from all counts I will get the intronic counts. When I did this (using the output filtered_feature_bc_matrix.h5 files, filtered for only cells and genes present in both files), I got some (~0.8%) negative values in my resulting matrix for intronic reads, meaning that for some cells/genes, more reads are counted without the --include-introns flag. I probably missed something, could you please explain why this happens? Or suggest an alternative way to obtain a matrix of intronic read counts without constructing a new reference?
Hi, I want to quantify separately exonic and intronic reads in my single-cell data. To do so, I have applied CellRanger to the same exact FASTQ files, with and without the
--include-intronsflag. I assumed that by subtracting the exonic counts from all counts I will get the intronic counts. When I did this (using the outputfiltered_feature_bc_matrix.h5files, filtered for only cells and genes present in both files), I got some (~0.8%) negative values in my resulting matrix for intronic reads, meaning that for some cells/genes, more reads are counted without the --include-introns flag. I probably missed something, could you please explain why this happens? Or suggest an alternative way to obtain a matrix of intronic read counts without constructing a new reference?Best, Binyamin