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Hi @mbrochut Have you tried to run it without the Velocyto option? |
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Hi @mbrochut what is the output in Summary.csv file? |
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Hello everyone!
First, thanks a lot for this wonderful tool.
I am working with Fixed RNA Profiling Probe from 10X and I am trying to do velocity analysis.
First I was doing it with the Velocyto package developed by Gioele La Manno but after running it, the output file was almost empty. I then realized that, with fixed cells, the sequencing is actually the probes and not the pre-mRNA that can be immature (unsplice) or mature (splice) and so, it is actually impossible to perform velocity analysis.
Before realizing that I could not do velocity analysis, I was trying to run it with STAR and I had some problems to create the output files.
I am running this command:
The alignment run successfully and I have a Log.final.out file but no : features.tsv, barcodes.tsv, matrix.mtx and splice/unsplice matrix.
I am using the output BAM file from CellRanger.
Is it due to my fixed sample or am I running it wrongly?
My Log.final.out:
If you could help me, I would gladly appreciate :)
ps: probes can target spliced or unspliced region so maybe we could infer some information about that.
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