Spatial transcriptiome analysis

Question

[siu]

Hi, I want to analyze the fastq files from spatial transcriptome. I know, I should use the Spaceranger count to do the alignment, but I am wondering if I have to do any quality filtering of the reads before doing the alignment (like bulk RNA) or just run the spaceranger on these files?

Thanks

[GenoMax]

While I don't have experience with spaceranger 10x software generally takes care of properly QC'ing data internally. I would say go ahead and run while we wait for someone with specific experience to answer.

[jv]

it should be fine to start directly with Spaceranger unless there is something really "off" about the raw sequencing data

[siu]

Thank you so much to both of you.