BD Rhapsody software - single cell seq

Question

[colindaven]

Dear all,

has anyone worked with BD Rhapsody single cell data before ?

According to this FAQ https://scomix.bd.com/hc/en-us/articles/360057714812-All-FAQ you can only use the analysis software online via sevenbridges. That is, you cannot download the tool and use it locally to reanalyze data (which is a fantastic way to get rid of customers by the way, great job).

I'm sure there are other alternatives with Dropseqpipe and others, but has anyone found a decent solution for these data ? Their library design does not seem that simple either with variable bases in the V2 scheme. https://teichlab.github.io/scg_lib_structs/methods_html/BD_Rhapsody.html

Thanks

Edit: so local usage is possible, as LChart says below.

You basically have to install common workflow language CWL using their PDF instruction guide, then download their repository of just yml and cwl files from here https://bitbucket.org/CRSwDev/cwl/src/master/. Then you edit the yaml files to point to your input files (should be easy).

The next step is running with eg

cwl-runner --outdir out1 rhapsody_wta_1.9.1.cwl template_wta_1.9.1.yml

and then experience cryptic CWL errors. I haven't been successful yet, and am not sure if the problem is with the CWL from BD Rhapsody, or the yml syntax from me (which appears valid).

Answer 1

[LChart]

Yes, BD Rhapsody can be run locally. In fact it uses a docker so the setup isn't really all that bad: https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD_Single_Cell_Multiomics_Analysis_Setup_User_Guide.pdf

If you are deploying somewhere without docker, you will run into trouble as one particular step of the pipeline calls docker from within docker, so no amount of reverse-engineering the environment can get around it.

It should be pointed out that the FAQ you link does not say the software must be used via the seven bridges platform; only that it cannot be downloaded from seven bridges itself:

You cannot download the software from Seven Bridges. Please follow the BD Single-Cell Multiomics Analysis Setup User Guide on installing the pipeline for local use.