GreenCells | 10X Genomics Upstream analysis

10X Genomics Upstream analysis

We provide Shell command line for plant single cell 10X Genomics upstream analysis.

Step1. Download software and prepare input data

  Download Software:
  Software Needed: cellranger.
  Preparation files:
  Under the project folder, there are all fastq raw data under the RawData folder (Sample_S1_L00X_R1_001.fastq.gz and Sample_S1_L00X_R2_001.fastq.gz must be included, while Sample_S1_L00X_I1_001.fastq.gz is optional.The sample name is replaced with a sample number that is different for each sample.L00X indicates that the parent library of the fastq file was run on lane L00X), and the GenomeAnno folder that stores the genome and annotation files of the corresponding species.

Step2. Make reference with cellranger 'mkref' command

Build references:
--out_dir : Output directory; --fasta : Reference genome path; --genes : Reference genome annotation file path. The entries for lncRNAs that overlapped protein-coding genes should be filed separately to avoid multiple-mapped; --nthreads : Maximum memory (GB) used when aligning reads with STAR.; --memgb : Maximum memory (GB) used when aligning reads with STAR.

--out_dir:

--fasta:

--genes:

--nthreads:

--memgb:

Step3. Quantification with cellranger 'count' command

Quantitative analysis:
--fastqs : Path to input FASTQ data; --transcriptome : Path of folder containing 10x-compatible transcriptome reference; --localcores : Set max cores the pipeline may request at one time; --localmem : Set max GB the pipeline may request at one time.

--fastqs :

--transcriptome :

--localcores:

--localmem :

Example:
nohup bash 10Xgenomic.sh &
Help instructions:
After running the Shell script, the project folder contains the following content:
RawData folder: stored raw data; GenomeAnno folder: genome files and annotation files; Refresult folder: species references information; FianlResult folder: contains quantitative results for different samples