Confused with 2 SRA runs for one sample


Hello, I am completely new to Sequencing and programming (and I am blonde) - so please bear with me.

I already saw that there are some questions about it, but I could not really understand/deduce what I have to do now.
So, I have the task to recreate some figures of a paper with RStudio. I choose the single-cell RNA-Seq results from this paper:
I already downloaded all SRA files via the SRAtoolkit and I am already converting them in FastQ files with the split-3 option. And I know I have to check them with FastQC afterwards.
But, there are for each sample two SRA runs (this sample for example:] )
Why are there 2 SRA files, which will result in ultematively in 4 FastQ files for one sample?
I have read somewhere "technical duplicates", but there is also this huge difference in size (6.9 GB and 18.3 GB) and if I am clicking on the runs to get more informations I get lost.

Can someone please explain to me why there are 2 SRA files are and how I should proceed with them?






With 10x data I recommend that you always try and get the original data submitted. It can be found under Data Access tab (one of your SRA recs) and for a change seems to be available at no cost via cloud (not always the case). Larger file would be the actual read and the smaller one cell barcode +UMI.

Both runs are for the same biosample. So they could be biological or technical replicates. See if there is more information in the publication.

Edit: Looking at the sample entry in GEO one could be scRNA-seq and other is TAP-seq sample.

Hey I am sorry for the long wait. Had/have quite a lot to do.

This was their one and only response:
"Each sample/library was run in two lanes of Hiseq, one full and 1/3 of another, thats why they have different size. if you want to run cellranger with the reads to replicate our study you would need to use both runs as an input."

before adding your answer.

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