How to preprocess GEO bulk RNAseq fastq file with salmon

[@jesusvaldeshernandez]

Hello Tommy, nice video!. I have a question about downloading RNAseq fastq files from SRA Run Selector using fastq-dl. For example, considering Accession ID GSE116951 (LibraryLayout: PAIRED-end) and Run SRR7511281, how can I get the two fastq files (foward and reverese) from the sample SRR7511281?

[@chatomics]

if you use fastq-dump instead, take a look at www.biostars.org/p/222122/

[@qhawenid]

Hi Tommy, Is there a way to evenly partition/ split samples to create pseudo-replicates for a scRNA seq dataset with one sample per condition?Thanks in advance!!

[@chatomics]

you can do random sample the cells github.com/satijalab/seurat/issues/243 and then use satijalab.org/seurat/reference/aggregateexpression

[@qhawenid]

@@chatomics Thank you for the timely feedback. Let me work on it.