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DESeq2 with salmon
Meg Staton edited this page Nov 13, 2022
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Get files
scp -r isaac:/lustre/isaac/proj/UTK0208/rnaseq/analysis/mstaton1/3_salmon/\*quant .
You really only need quant.sf for each sample but this keeps directory structure in order which makes R code easier
Get other stuff to build your transcript to gene conversion data:
scp -r isaac:/lustre/isaac/proj/UTK0208/rnaseq/raw_data/Ppersica_298_v2.1.gene_exons.gtf .
scp -r isaac:/lustre/isaac/proj/UTK0208/rnaseq/raw_data/Ppersica_298_v2.1.transcript.fa .
scp -r isaac:/lustre/isaac/proj/UTK0208/rnaseq/raw_data/Ppersica_298_v2.1.gene_exons.gff3 .
scp -r isaac:/lustre/isaac/proj/UTK0208/rnaseq/raw_data/salmon_transcripts_index .