Input Data

Follow these instructions to populate input files to successfully run the solosis CLI.

Samplefile

Several commands in Solosis accept a --samplefile option where you can pass multiple samples as a comma-separated .csv or tab-separated .tsv file. The column that contains the Sample IDs would be called “sample_id”.

sample_id
s12345
s67890

Cell Ranger ARC Libraries File

Cell Ranger ARC requires a specific input file, called a libraries file, which is a comma-separated variable csv file. Construct a 3-column libraries CSV file that specifies the location of the ATAC and GEX FASTQ files associated with the sample. For example:

fastqs	sample	library_type
/home/jdoe/runs/HNGEXSQXXX/outs/fastq_path	s12345	Gene Expression
/home/jdoe/runs/HNATACSQXX/outs/fastq_path	s67890	Chromatin Accessibility