Running tracer on 10x Genomics data

Teichlab / tracer

TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data

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Running tracer on 10x Genomics data #111

Closed abiswas97 closed 3 years ago

abiswas97 commented 3 years ago

I'm trying to use tracer on some 10x genomics fastq files, and noticed I'd have to demultiplex them to be used.

I found this thread (https://github.com/Teichlab/tracer/issues/58) from a couple years ago that mentioned tracer hadn't been validated for 10x data. Have their been any updates on this? Will demultiplexing using something like Sabre provide reliable output, or is this not recommended?

mstubb commented 3 years ago

Hi,

No, TraCeR still isn't recommended/intended for use with 10x data. You could try Sabre but I haven't got any experience with it.

Very best,

Mike