Instructions to Download and Process FASTQs of 1.3M Brain Cells

Technical Note, Last Modified on June 23, 2017, Permalink

Due to the large size of the data (3.6 Terabytes), the raw data will not be available directly from our website. Users can download the raw fastq data from Amazon S3 at their cost using the 'Requestor Pays Bucket' option. (Depending on user's Amazon region, Amazon may charge up to ~$350 for this data transfer). Interested users should follow the steps here to download and process the FASTQ files.

1. Download the files

2. Extract the fastqs

3. Run the count pipeline

4. Run the aggregator pipeline

5. Run the reanalyze pipeline:

cellranger reanalyze --id=neuron_reanalyze --matrix=/path/to/aggregator/neuron_aggregation/outs/filtered_gene_bc_matrices_h5.h5 --params=reanalyze.csv (NOTE: this uses >300GB RAM - it was run at 10x on a machine with 384GB RAM)