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alexdobin / STAR

RNA-seq aligner
MIT License
1.87k stars 506 forks source link

application of star solo #1854

Open saassli21 opened 1 year ago

saassli21 commented 1 year ago

Thank you for providing this fascinating tool. I do have a question regarding its application. Is the STAR Solo tool only applicable for human and mouse cells, as it is the case with Cell Ranger? I noticed that in your recommendations, it is mentioned that we have to specify the 10x Chromium v1, v2, v3 config parameters. If STAR Solo is not limited to human and mouse cells, how could we use this tool for analyzing bacterial or fungal cells, for example?

Thanks, Safa,

alexdobin commented 1 year ago

Hi Safa,

for any species of interest, you would need to generate STAR genome index using the species-specific FASTA and GTF (annotation) files.

saassli21 commented 1 year ago

@alexdobin what about 10x Chromium v1, v2, v3 config parameters. we utilize the same config files for any species ? or each species has it's own versions of config file

alexdobin commented 1 year ago

The 10X technology parameters do not depend on the species.