ucsc_human_cortex.md

Developing human cortex data

This dataset contains ~4200 cells from the developing human cortex sequenced with Fluidigm C1, with relatively high coverage reads.

Paper: Nowakowski et al 2018)

Contact point in HCA: Max Haeussler [email protected], Jim Kent (UCSC), data produced/analyzed by Tom Nowakowski, Aparna Bhaduri (UCSF)

Data includes

1. TPMs from HISAT2

2. Metadata csv includes clustername, age, patient ID.

    wget http://cells.ucsc.edu/aparna/matrix.tsv.gz
    wget http://cells.ucsc.edu/aparna/meta.tsv

As written above, the matrix was made with HISAT2 and contains TPM values. See manuscript for details or contact Aparna Bhaduri for alignment pipeline details.

The original FASTQ files are in dbGAP

Browser: http://cells.ucsc.edu