Open source alternatives to SureCell RNA Single-Cell App in Basespace?

Question

[greener]

I have some single Cell data obtained from a ddseq / Illumina. I would prefer to process this data on my linux server instead of base space. (Base space costs money). Any alternatives instead of using SureCell RNA Single-Cell App in Basespace ? I looked around and couldn’t find anything. Any suggestions are appreciated . Thanks -Rich

[GenoMax]

I am not sure what SureCell is but you can find everything related to single-cell RNAseq data analysis at this link.

[greener]

Sure Cell is illumina’s single Cell system with Bio-Rad.

http://www.bio-rad.com/en-hr/product/ddseq-single-cell-isolator?ID=OKNWBSE8Z

So far it seems the only way to generated useable data for analysis is to run it through base space. I’m hoping to find some open source options. Thanks

[GenoMax]

If you are able to generate fastq data for your samples (along with relevant index information) then you should be able to use an independent tool from the collection above. Someone may come along and confirm if they have been able to do that.

Answer 1

[allthebases]

There is a SureCell RNA Data Analysis tech note that describes the BaseSpace App workflow with some detail:

• https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/single-cell-rna-data-analysis-tech-note-1070-2017-001.pdf

Hopefully that can help you make some progress if you plan to implement your own pipeline. Alternately, I suggest reach out to Illumina Tech Support ([e-mail]) or your lab's dedicated Illumina Field Application Scientist for some suggestions on how to analyze your data without using BaseSpace Sequence Hub.

Source - I work at Illumina :)

Answer 2

[ibseq12]

ddseeker at https://github.com/cgplab/ddSeeker