Single-cell RNA-Seq pipeline

scRNA-seq pipeline for aligning reads generated from SeqWell/DropSeq protocols. Much of this is taken directly from the McCarroll Lab's alignment cookbook

Run dropseq pipeline

bash scrna.preprocess_master.sh -d {raw_directory}

arguments:
d=[d]irectory with raw data (directory; required)  
g=directory with the reference [g]enome  
    accepted values: GRCh98, Mmul_8  
e=[e]mail address

Run cellranger

Each sample should be seperated in one folder. The name of the folder should match the SampleID
ex. rawDir/SampleID/SampleID_S1_L001_I1_001.fastq.gz
rawDir/SampleID/SampleID_S1_L001_R1_001.fastq.gz
rawDir/SampleID/SampleID_S1_L001_R2_001.fastq.gz
...
where rawDir is the parent directory with the raw FASTQ files, and SampleID sample id

bash cellranger.master.sh -d {raw_directory}

arguments:
d=parent [d]irectory with raw data; each sample must be seperated in a
  seperated directory; the subdirectory name will be used as sample id
  (required)
g=directory with the reference [g]enome
  accepted values: GRCh98, Mmul_10