SRA scRNAseq data from 10x - cellranger count vs aggr

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3.3 years ago

essiggurke • 0

Hello,

I downloaded a bunch of runs for one SRA experiment using fastq-dump/esearch and want to reanalyse it. My problem now is that I don't know which of these can be used in the cellranger count pipeline together and which need to be counted separately and then aggregated (bc they are from different libraries or flowcells).

Edit: this is the dataset

https://www.ncbi.nlm.nih.gov/sra?term=SRX5411289

When I go to the top left and select full-xml instead of full, I get alot more information, including the upload file names. These suggest that some runs were from the same lane while others weren't. Should I only process the run files from the same lane in one cellranger count pipeline or can I assume that all runs from one SRA experiment are from one sample and one library and can be analysed together ?

Sorry for the kind of basic question, I am new to 10x datasets.

Best, essiggurke

RNA-Seq 10x • 942 views

ADD COMMENT • link 3.3 years ago by essiggurke • 0

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Entering edit mode

Can you link the dataset? One cannot tell in general as it is on the authors how they label data. That might or might not be intuitive sometimes. Kudos for the username by the way :)