Creating a seurat object from E-MTAB-8560
Can someone help me understand how I can create a seurat object from this (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-8560) RNA-seq study? I've downloaded the submitted fastq files but I'm not sure what the "library or feature type" is for cellranger, and it fails when I try. Tried queryAE in R but it is deprecated.
Any help would be appreciated.
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This is not a 10x dataset. It is SMART-seq2. There are thousands of samples in the study: https://www.ebi.ac.uk/ena/browser/view/PRJEB36252 or see at NCBI: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=2&WebEnv=MCID_6494795c61aef326ed920080&o=acc_s%3Aa
There is 3.5TB of data so when you say you downloaded fastq files did you do so for one sample?
Yes, I downloaded fastq files from one sample.
What can I do to analyze this data then?
You can use:
Link --> https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README/
Link --> https://nf-co.re/smartseq2