Question: Open source alternatives to SureCell RNA Single-Cell App in Basespace?
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gravatar for greener
2.5 years ago by
greener10
United States
greener10 wrote:

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

ADD COMMENTlink modified 14 months ago by ibseq120 • written 2.5 years ago by greener10
1

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

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax90k

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

ADD REPLYlink written 2.5 years ago by greener10

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax90k
0
gravatar for allthebases
2.5 years ago by
allthebases0 wrote:

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

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 (techsupport@illumina.com) 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 :)

ADD COMMENTlink written 2.5 years ago by allthebases0
0
gravatar for ibseq12
14 months ago by
ibseq120
London
ibseq120 wrote:

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

ADD COMMENTlink written 14 months ago by ibseq120
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