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PierreBSC / Viral-Track

MIT License
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Starting from 10x Cell Ranger output #2

Closed zji90 closed 4 years ago

zji90 commented 4 years ago

Hi, I wonder if I already have my data processed using 10x Cell Ranger software (which also uses STAR to do the alignment), is there a way I can run Viral-Track from Cell Ranger output so that I can avoid redoing the alignment again? Thanks!

PierreBSC commented 4 years ago

Hi Zhicheng,

Unfortunately you can not use the STAR alignment performed by Cell Ranger as it (usually) is not performed using a exhaustive database of viral sequences included in the reference genome.

In the case you added the reference viral genomes to the STAR index and then performed Cell Ranger demultiplexing, the Viral-Track main script could be then be modified to directly process the bam file, but so far this feature does not exist !

Best

Pierre

zji90 commented 4 years ago

Thank you!

GhobrialMoheb commented 2 years ago

@PierreBSC , is there an update on potential use of cell ranger BAM files as an input ?