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epigen / scifiRNA-seq

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UMI count matrix #10

Open somnathtagore opened 3 years ago

somnathtagore commented 3 years ago

Hi André,

Fortunately, based on your previous advices, scifi pipeline is running. We are getting feature count matrices as output. Is there a way in which we could get UMI-count matrices ? Does scifi has any inbuilt tool that can generate it ? Or do we need some other tools like umi-tools etc to do that ?

Thank you. Som

perllb commented 3 years ago

May I ask what matrix you are getting as output? When I dry-run my scifi map, I only get STAR + featureCounts output (including gene-tagged .bam file). As I understand, there should also be a h5 matrix as well as csv files with metrics pr barcode?