indrop

Indrops analysis pipeline at BioCore@CRG

The pipeline is based on the DropEST tool: https://github.com/hms-dbmi/dropEst

The current supported version is v1 & v2

• File 1: barcode reads. Structure:
  • Cell barcode, part 1
  • Spacer
  • Cell barcode, part 2
  • UMI
• File 2: gene reads

The pipeline

1. QC: Run FastQC on raw reads. It stores the results within QC folder.
2. Indexing: It makes the index of the genome by using STAR.
3. dropTag: It creates a "tagged" fastq file with information about the single cell that originated that read in the header.
4. Alignment: It aligns tagged reads to the indexed genome by using STAR. Reasults are stored in Alignments folder.
5. dropEst: It provides the estimation of read counts per gene per single cell. The results are in Estimated_counts folder and consists of an R data object, a file with a list of cells (aka barcode combinations), another with a list of genes and a matrix in Matrix Market format (https://en.wikipedia.org/wiki/Matrix_Market_exchange_formats).
6. dropReport: It reads the R data oject produced by the dropEst step to produce a quality report. It needs a list of mitochondrial genes.
7. multiQC: It wraps the QC from fastQC and STAR mapping in a single output.