Forum:Spaceranger missing spatial coordinates [Discussion]
0
0
Entering edit mode
3 months ago
morovatunc ▴ 550

Hi,

I dont know how to do this without pointing out specific PIs or studies. Therefore, I apologise for not being clear.

10x Visium platform has two input.

1) Expression (h5 or mtx/barcodes/features

2) Spatial directory (scalefactor, low/hi images, tissue_positions.list.csv)

If one requires minimum input, one of #1 inputs and tissue_positions_list.csv would be sufficient.

I started to see some projects share only expression information without giving anything related to #2.

Given barcodes always located in the same array_row, array_col. I was wondering if it would be okay to use tissue_positions_list.csv of one of example 10X datasets?

Thank you for the discussion,

Best regards,

T.

Visium • 544 views
ADD COMMENT
0
Entering edit mode

I started to see some projects share only expression information without giving anything related to #2.

Are you referring to publicly available data in a repository like SRA?

ADD REPLY
0
Entering edit mode

Yes. GSE/GEO accessions. Processed data. h5 shared.

ADD REPLY
1
Entering edit mode

SRA was designed to host only sequences and since then we have had a proliferation of additional datatypes that can't go into this database.

Partly it is on submitter's to include this additional information (NCBI does not enforce it AFAIK). This is how the original 10x BAM files are sometimes available under Data Access tab in SRA record. This spatial data could very well be submitted and made available there.

ADD REPLY

Login before adding your answer.

Traffic: 1469 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6