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velocyto-team / velocyto.py

RNA velocity estimation in Python
http://velocyto.org/velocyto.py/
BSD 2-Clause "Simplified" License
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How to apply on Illumina HiSeq? #160

Open wang950312 opened 5 years ago

wang950312 commented 5 years ago

I' m very interested in your team' s project, but the data I had was seqenced by Illumina HiSeq2000 for per cell. I read the pipline and found that the folder structure more similar to the smart-seq platform: one sample have several cells same as one well have several cell. So could I apply your plpline on my data?

Nithishwer commented 4 years ago

Hi,

I am facing a similar situation. Did you have any progress on using the Velocyto pipeline with Illumina?

Thanks, Nithish

Nithishwer commented 4 years ago

Turns out the SRA data used was from the 10x platform. I Used Cell Ranger count on the fastq file and performed a velocyto run on the resulting BAM file.