How would I input the count matrices per sample files into Monocle3?

Question

[Pratik]

Hello,

I hope you are safe and well.

How would I input the count matrices per sample files into Monocle3?

I thought Monocle3 requires for input only three files (expression_matrix, cell_metadata, gene_annotation) or the three files generated from cellranger? How would I use the individual cell sample files in Monocle3?

This is the data I wish to use:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110154

I believe the count matrices per sample are within the supplementary RAW file: GSE110154_RAW.tar in individual .csv files.

Very Respectfully, Pratik

[GenoMax]

It is unclear what technology this data is from (my guess is it is some plate based technology like Fluidigm, so this is not 10x, so no cellranger files). The actual fastq data files seem to be paired-end (64 bp, which is an odd length). Here is one example sample (click on Data access tab to see the original fastq files). Since there are 1800+ samples this is going to be a rather large undertaking.

Edit: A second sample seems to have paired-end 129 bp reads. Well that is going to make this even more complex.

[Pratik]

Thank you genomax.

Okay so no cellranger for the fastq files. I'm actually going to look at the group's previous papers' materials and methods section to see how they did their previous scRNA-seq study. Perhaps it could reveal some clues on how to analyze this data.

Thank you again.

I would have been trying to jam the fastq files into cellranger haha! Thank you for saving me the time!

Very Respectfully, Pratik

Answer 1

[ATpoint]

It looks like they really uploaded one count matrix (or rather one column) per assayed cell. I'd simply download all, cbind them together (with only the first column being the gene names of course) and then input it as you'd do with any normal count matrix. Does that make sense for you since I did not really read through all these files so I am not sure how these uploaded files are related?

[Pratik]

Thank you ATpoint.

Yes this does make sense. I'm going to learn cbind and also read the previous scRNA-seq study this group did, to see how they did it.

The 1860 files are the 1860 different cell types gathered from gestational stages from weeks 12 to 22. (Sorry if I stated the obvious).

Thank you again!

Very Respectfully, Pratik

[Pratik]

Hi ATPoint,

I got as far as aggregating the data using cbind and making one file of all the data. I am just not sure how the data is supposed to exactly look for it to be inputted into Seurat. Do you think you could share your insight on this in my new question, please?

What is a count matrix for input into Seurat supposed to look like?

Very Respectfully, Pratik