Question about the ViralAnalysis part of the analysis

[GhobrialMoheb]

Hi @RachellyN
Good day, I would like to ask you for a clarification of the steps performed in the "ViralAnalysis" section.

• Was the 1st step is to perform the Viral-Track analysis (as described in:https://github.com/PierreBSC/Viral-Track) ?

• Did you use the cellranger generated FASTQ files for further downstream analysis directly or did you do the pre-processing described in the "Pre-processing of the single data" section of (https://github.com/PierreBSC/Viral-Track)?
  (cellranger generated FASTQ files are described: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/mkfastq)

• Was your "Summary_viral_enrichment.py" analysis performed on the output of the Viral-Track analysis ?
  (may you please describe the steps from Viral-Track analysis to have the viral data in your single cell object metadata?)

Thanks alot
Moheb