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LuyiTian / scPipe

a pipeline for single cell RNA-seq data analysis
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Support for BCLs #101

Open AMChalkie opened 6 years ago

AMChalkie commented 6 years ago

As your neighbours at AGRF produce BCLs for CellRanger, it would be useful to integrate preprocessing from BCLs to fastq to make things more seamless and keep all analysis within a single framework.

(Nice project by the way, I really appreciate the work).

DarioS commented 6 years ago

Yes, please!

Shians commented 6 years ago

I have only converted from raw BCL once myself, perhaps @LuyiTian can look into this. As far as I know this can be done by wrapping around bcl2fastq, the difficult part is getting the correct settings into the required XML sheet, I recall doing quite a bit of googling to get that right. Perhaps the basecallQC bioconductor package can help with that. The other option would be to wrap the 10X wrapper for bcl2fastq mkfastq.

That or I can write up a script that generates a nice email asking AGRF to process the BCL into fastq since it should be quite routine from their end. 😛

LuyiTian commented 6 years ago

I think bcl2fastq or mkfastq already do a good job on this. I used bcl2fastq myself. The documentation is not good though so I also spend time googling how to set up correctly. I might be worth to have a script or a tutorial on how to use them to get correct fastq files.

AMChalkie commented 6 years ago

A script or tutorial would be very useful!