I used an
nf-core/rnaseq pipeline using
star_salmon default aligner, on strand specific dataset. I have a question about gene counts data obtained as a result of salmon quantification. I am interested in gene counts for downstream only rather than isoforms. It seems like the nf-core rnaseq pipeline is designed to import "counts_gene_length_scaled" reference 1 reference 2 via
tximport > Deseq2 > size_factors > vst. The pipeline generates a number of files, I would like to know which file from the shown below is best to use in
edgeR DGEList. Probably this file "salmon.merged.gene_counts.rds"?
Before using this pipeline I used to get started from the raw gene counts from
featureCounts then use in EdgeR.
salmon.merged.gene_counts_length_scaled.tsv salmon.merged.gene_counts.rds salmon.merged.gene_counts_scaled.rds salmon.merged.gene_counts_scaled.tsv salmon.merged.gene_counts.tsv salmon.merged.gene_tpm.tsv salmon.merged.transcript_counts.rds salmon.merged.transcript_counts.tsv salmon.merged.transcript_tpm.tsv salmon_tx2gene.tsv