Demultiplexing inDrop dataset

Question

[ATRX]

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!

Answer 1

[Zhaorong]

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.

[jade]

Hello, The page "https://iccb.med.harvard.edu/files/iccb/files/sequencing_indrops_libraries_02_28_18.pdf" cannot be found. Could you please share an updated link?