Sample Bam File - Githubissues

velocyto-team / velocyto.py

RNA velocity estimation in Python

http://velocyto.org/velocyto.py/

BSD 2-Clause "Simplified" License

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Sample Bam File #119

Open shaaaarpy opened 6 years ago

shaaaarpy commented 6 years ago

Can someone please post the sample .bam file for the velocyto python notebooks for which i can myself generate the loom file.

Suger0917 commented 6 years ago

I run velocyto in the command line but not in the notebooks. Please make sure that bam files containing CB and UB tag: If the bam files didn't containing these tag, you can use python package 'simplesam' to add them.https://github.com/velocyto-team/velocyto.py/issues/107

EularTang commented 6 years ago

Maybe you can use the data followed to practise, which generated by 10X. https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neurons_900

denvercal1234GitHub commented 3 years ago

@Suger0917 -- My bam file does have CB and UB as you boxed in your comment back in Sep 25 2018 above, but it still gives me the error "the bam file does not contain cell and umi barcodes appropriately formatted. If you are running UMI-less data, you should use the -U flag" . Any idea? Should I still use "simplesam"?

I tried various things to solve this as described in #320.

Thank you for your help!