This repository contains Python scripts used for scPLATE-Seq data processing

demultiplex.py

Python scripts for demultiplexing sequencing result into individual .fastq files corresponding to each well

Inputs:

--workDir, -d: Working directory

--barcodeInfo, -i: Tab-delimated text file specifying barcode-well correspondence, with barcodes (8nt) in 1st and wells in 2nd column

--barcodeLen, -l: Length of cell barcode

--umiLen, -u: Length of UMI

--seqFastq, -s: Multiplexed sequencing result in .fastq file containing the mappable (5') reads

--barcodeFastq. -b: Multiplexed sequencing result in .fastq file containing the barcoding (3') reads

--prefix, -p: Prefix of demultiplexed .fastq files

Output:

Individual .fastq files corresponding to each well

CountUMI.py

Python scripts for measuring transcripts per gene and mapped reads per gene for single well

Input:

--samFile, -i: Result of STAR alignment with option --quantMode TranscriptomeSAM and --clip5pNbases 8 (8nt unmappable barcodes)

--umiFile, -u: Name of file containing transcripts per gene

--countFile, -c: Name of file containing mapped reads per gene

--lenUMI, -l: UMI length

hammingThreshold, -t: Hamming distance correction threshold, under which two UMIs are considered as from the same transcript, 0 if not applying hamming distance correction

Outputs:

Tab-delimated text files containing transcripts per gene and mapped reads per gene, with genes in 1st and values in 2nd column