This Drop-seq tool extracts reads per cell barcode (=the number of reads for XC tag in a BAM file).
Based on these, a cumulative distribution plot is drawn. This plot can be used to estimate how many cells you want
to extract from your BAM in the DGE matrix: the inflection point or the "knee" of the distribution shows this.
The estimate of the inflection point is also given in the inflectionPoint.txt file. The estimation is done using the "inflection" package in R.
The number of STAMPs are the number of cell barcodes to the left of the inflection point (the "knee"); to the right of the inflection point are the empty beads that have only been exposed to ambient RNA.
For more details, please check the Drop-seq manual. We would like to thank Dawit Yohannes for his kind assistance with the development of this tool.