parse-pipeline
Summary
Module Name: parse-pipeline
Support Level: Primary Support
Software Access Level: Open Access
Home Page: https://www.parsebiosciences.com/
Software Description
Split-pipe is the software developed by Parse Biosciences for demultiplexing sample and cell combinatorial barcodes and aligning transcript-derived reads to the genome. Split-pipe produces a cell-by-gene counts matrix containing the expression of each gene for each cell barcode, along with a quality report detailing the number of valid cell barcodes that were found, median numbers of genes and transcripts per cell, and read alignment statistics to the genome. MSI provides selected reference files that are compatible with split-pipe in the bioref database in this directory:
/common/bioref/splitpipe_parse/
General Linux
Depending on where you are working, there may be more than one version of Parse split-pipe available. To see which modules are available for loading you can run:
module avail parse-pipeline
This will provide a list of all versions of the package, shown as parse-pipeline/
To load a specific module for use in a Linux environment, run the command:
module load parse-pipeline/<version>
For example, you can use the command module load parse-pipeline/1.5.0 to load version 1.5.0
which is the current version available on our system.
To launch the package and view the help menu after it is loaded, use the command:
split-pipe -h
Example SBATCH Script
In the following example we run a single Parse sublibrary FASTQ file through split-pipe to
demultiplex the samples and cells given in a text file called samplelist.txt that
indicates which Parse plate wells correspond to each sample.
Example of a samplelist.txt file (column 1 = sample name, column 2 = plate well numbers, and columns are tab-delimited):
Sample1 A1-A6
Sample2 A7-A12
Sample3 B1-B6
Sample4 B7-B12
Sample5 C1-C6
Sample6 C7-C12
Sample7 D1-D6
Sample8 D7-D12
Example split-pipe_run.sbatch script:
############split-pipe_run.sbatch############
#!/bin/sh
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 32
#SBATCH --mem=200G
#SBATCH -t 96:00:00
#SBATCH -p msismall
#SBATCH -A YOUR_GROUP
#SBATCH --mail-type="ALL"
#SBATCH --mail-user=YOUR_EMAIL@umn.edu
# Load the parse-pipeline module
module load parse-pipeline/1.5.0
R1_FASTQ="Sub_Library1_L004_R1_001.fastq.gz" # Name of the R1 sublibrary FASTQ file
R2_FASTQ="Sub_Library1_L004_R2_001.fastq.gz" # Name of the R2 sublibrary FASTQ file
FASTQ_DIR="/path/to/your/FASTQ/folder/" # The path to your folder of FASTQ files
OUT="split_pipe_output/Sub_Library1" # The name of the split-pipe output folder
split-pipe --mode all \
--genome_dir "/common/bioref/splitpipe_parse/1.5.0/mm39/" \
--fq1 ${FASTQ_DIR}/${R1_FASTQ} \
--fq2 ${FASTQ_DIR}/${R2_FASTQ} \
--output_dir ${OUT} \
--samp_list samplelist.txt \
--chemistry v3 \
--kit WT \
--chem_score_skip \
--kit_score_skip \
--no_keep_going \
--nthreads 32
Once all of the sublibraries are processed using “split-pipe –mode all”, they can be
combined together to produce the final output using the split-pipe --mode comb command.
Here is an example sbatch script:
############split-pipe_comb.sbatch############
#!/bin/sh
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 32
#SBATCH --mem=100G
#SBATCH -t 96:00:00
#SBATCH -p msismall
#SBATCH -A YOUR_GROUP
#SBATCH --mail-type="ALL"
#SBATCH --mail-user=YOUR_EMAIL@umn.edu
module load parse-pipeline/1.5.0
# combine the split-pipe output directories from each sublibrary listed in "subsample.list"
split-pipe --mode comb \
--sublib_list subsample.list \
--output_dir split_pipe_output/combined \
--nthreads 32
The subsample.list file contains a list of all of the sublibrary output folder names produced from the split-pipe runs above. For example:
/path/to/your/split_pipe_output/Sub_Library1
/path/to/your/split_pipe_output/Sub_Library2
/path/to/your/split_pipe_output/Sub_Library3