dropEst - Pipeline

Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements.

If you have problems with installation, please look at the Troubleshooting page and open an issue if there is nothing.


[0.8.6] - 2019-08-01

  • Added support for Drop-seq and CEL-Seq2

See Changelog for the full list.

General processing steps

  1. dropTag: extraction of cell barcodes and UMIs from the library. Result: demultiplexed .fastq.gz files, which should be aligned to the reference.
  2. Alignment of the demultiplexed files to reference genome. Result: .bam files with the alignment.
  3. dropEst: building count matrix and estimation of some statistics, necessary for quality control. Result: .rds file with the count matrix and statistics. Optionally: count matrix in MatrixMarket format.
  4. dropReport - Generating report on library quality.
  5. dropEstR - R pacakge for UMI count corrections and cell quality classification


Complete examples of the pipeline can be found at EXAMPLES.md.

Here are results of processing of neurons_900 10x dataset.

Supported protocols

  • 10x
  • CEL-Seq2
  • Drop-seq
  • iCLIP
  • inDrop (v1-3)
  • Seq-Well
  • SPLiT-seq