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yjzhang / split-seq-pipeline

MIT License
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Input files for testing the pipeline #15

Closed michael-kotliar closed 4 years ago

michael-kotliar commented 4 years ago

Hello, I'm trying to use your pipeline, but I couldn't find any input files, that I could use as an example. Would you mind providing some links on the files that I can use as input_R1.fastq.gz and input_R2.fastq.gz

Thanks a lot!

yjzhang commented 4 years ago

Some examples of test files are at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110823.

If you use these files, you should probably use the argument "--chemistry v1".

michael-kotliar commented 4 years ago

Thank you for the quick response. Would you mind providing an example of the command if I want to process GSM3017262 for example? I'm more interested in what should I set as --sample and --sublibraries parameters in the all and combine steps.

Thanks a lot

yjzhang commented 4 years ago

I don't think you need to use those parameters; the default parameters should work.

michael-kotliar commented 4 years ago

Cool, thanks a lot!