dropEst - Pipeline

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


[0.8.5] - 2018-11-14

  • Fixed several bugs
  • Support for SPLiT-seq
  • dropTag now able to trim and filter gene reads based on quality
  • Pipeline can be installed with make install

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 - UMI count corrections, 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
  • inDrop
  • iCLIP
  • SPLiT-seq
  • Seq-Well
  • Drop-seq