Tools for Visium 10x data alignment on a reference genome

Question

[Sergio]

Hello,

I was surprised that I did not find in literature any other tool rather than spaceranger for mapping Visium10x data on a reference genome.

I saw that some steps of STtools (https://academic.oup.com/bioinformaticsadvances/article/2/1/vbac061/6680241) could do the job, but it assumes that the user provides the SeqScope data format (with 3 different fastqs, as far as I understood). Now, I have two questions:

1. Can standard fastqs from Visium 10x be converted in SeqScope data format? It yes, how?
2. Is there any other aligner that can do the job?

Thank you very much.

[GenoMax]

FIle formats for SeqScope are described here: https://github.com/seqscope/STtools/blob/main/doc/fileformats.md

[Sergio]

Hello GenoMax,

Thank you for your reply. I also saw that description. My concern is more about having or not that kind of files when you analyze a Visium 10x dataset (they do not seem to be the same) and, in case, how to convert to SeqScope format.

[GenoMax]

This package is not documented well and the paper makes it sound like the package will create the input files needed automatically. Have you tried doing that?

The confusing part is about mention of 1st-seq fastq and 2nd-seq fastq. AFAI can tell visium generates only two files. First file with the spatial barcode+UMI and second file with cDNA. Out of the first file they are designating first 20 bases as HDMI, which need to be extracted.

[Sergio]

There is no option for creating the suited input files... And I am pretty sure that standard fastqs from Visium 10x does not show the requested features for being analyzed by STtools...

I think I will write to the authors for further clarifications, and I'll eventually update this thread in order to be useful for the community.

Thanks for your help