indropCounts: A function to handle a indrop V2 single cell data

In kendomaniac/CASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

A function to handle a indrop V2 single cell data

Description

This function executes a docker that produces as output the sinngle cell counts from V2 indrop single cell sequencing

Usage

indropCounts(
  group = c("sudo", "docker"),
  scratch.folder,
  fastq.folder,
  index.folder,
  sample.name,
  split.affixes,
  bowtie.index.prefix = "genome",
  M = 10,
  U = 2,
  D = 400,
  low.complexity.mask = "False",
  umi.threshold = 3
)

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
scratch.folder	a character string indicating the path of the scratch folder
fastq.folder	a character string indicating the folder where input data are located and where output will be written
index.folder	a character string indicating the folder where transcriptome index was created with indropIndex.
sample.name	the string indicating the sample name
split.affixes	the string separating SAMPLENAME from the Rz_001.fastq.gz
bowtie.index.prefix	the prefix name of the bowtie index. If genome was generated with indropIndex function the bowtie index is genome (default).
M	Ignore reads with more than M alignments, after filtering on distance from transcript end.
U	Ignore counts from UMI that should be split among more than U genes.
D	Maximal distance from transcript end, NOT INCLUDING THE POLYA TAIL.
low.complexity.mask	low complexity mask False (default) or True
umi.threshold	the minimal number of UMI to consider a gene present

Author(s)

Raffaele Calogero and Riccardo Panero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy

Examples

## Not run: 
system("wget 130.192.119.59/public/testMm_S0_L001_R1_001.fastq.gz")
system("wget 130.192.119.59/public/testMm_S0_L001_R2_001.fastq.gz")
library(rCASC)
#running indropCounts
indropCounts(group="docker", scratch.folder="/data/scratch", fastq.folder=getwd(),
       index.folder="/data/genomes/mm10indrop",sample.name="testMm",
       split.affixes="S0_L001", bowtie.index.prefix="genome",
       M=10, U=2, D=400, low.complexity.mask="False", umi.threshold=3)

## End(Not run)

kendomaniac/CASC documentation built on June 30, 2024, 3:27 a.m.