Confused with 2 SRA runs for one sample

2

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: www.ncbi.nlm.nih.gov/pmc/articles/PMC8077299/
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: www.ncbi.nlm.nih.gov/sra/SRX8998846%5Baccn] )
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?


runs


Illumina


RNASeq


sra

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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."


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