Question

Demultiplexing inDrop dataset

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Entering edit mode

4.7 years ago

Ar ★ 1.1k

Hello Everyone,

I am having issues with demultiplexing a publically available dataset on SRA (https://www.ncbi.nlm.nih.gov/sra/SRX4061030). It is a single-cell inDrop dataset and would like to know what is the best way to demultiplex it.

Any advice or help would be appreciated.

Thanks!

RNA-Seq single-cell in-Drop dataset • 1.2k views

ADD COMMENT • link updated 4.7 years ago by Zhaorong • 0 • written 4.7 years ago by Ar ★ 1.1k

score 0 · Answer 1 · 2020-01-07

Hi Ar, Based on what is showing on the SRA Run Browser, this is a inDrop v3 dataset which means the data consists four file: read 1 is the RNA sequencing, Read 2 is the cell barcode part 1, Read 3 is the library index for cell barcode and Read 4 is the cell barcode part 2 + UMI (Full introduction here: https://iccb.med.harvard.edu/files/iccb/files/sequencing_indrops_libraries_02_28_18.pdf). In this case you need the 8 base long library indices to demultiplex it.