GeoMX NGS RNASeq data analysis

Question

[Nai]

I am new to learn GeoMX data analysis. To learn this data analysis I am using GeoMX data (.fastq format) of kidney from GeoMX website. I went through manual but bit confused with quality filtering using GeoMX DSP or GeoMX NGS pipeline...I need help to get detailed guidance for this data analysis. Like Should i go as quality filtering in RNASeq or scRNASeq. There are some DCC file . (Will these file generated by machine or How will I use it in analysis

[Ram]

Use relevant keywords as tags, don't copy-paste the title. That's just lazy work.

[Nai]

Dear Sir,

This is the query for me as well as I understood these keywords appropriately for query

[Ram]

Your tags (before I corrected them) had all the words in your post title. That is not optimal. Please read online on how to choose appropriate subject matter keywords for a question.

Answer 1

[GenoMax]

DCC (count) files are generated by the geomxngspipeline software that is supplied by nanostring. Raw fastq data is processed though this software. Once these count files are generated (there is one file per ROI, they are compressed into a single zip archive for an experiment). This archive is then uploaded to the DSP software (on instrument) for associating with regions of interest that you selected/sequenced. DSP software offers an internal option to simply do the data analysis in the DSP software itself using a point/click interface. Some might find this limited but it will get you some results.

You also have the option of exporting the raw counts file associated with the ROI and then do your own analysis outside the DSP software.

If you are working with a core/provider then they should be able to assist you with all of this.

[Nai]

Thank you. I have few queries :

As you told "You also have the option of exporting the raw counts file associated with the ROI and then do your own analysis outside the DSP software". What will be the pipeline or workflow for analysis? Is geomxngspipeline default pipeline to generate the raw counts. or I can generate it by using fastq files.

[GenoMax]

AFAIK you have to use the geomxngspipeline for generating the counts since they need to be in a format that DSP software wants (you need to associate them with ROI and get the annotation).

Spatial transcriptomics is still a fluid field so I am not sure if there are standard workflows but I see this: https://www.bioconductor.org/packages/release/bioc/vignettes/GeomxTools/inst/doc/GeomxSet_coercions.html

Also options in --> Spatial Transcriptomics : Nanostring GeoMx DSP