A 3' tagged RNAseq method was used to sequence my data, I then used Salmon for mapping and quantification. My question is about using tximport for downstream DESeq2. In the tximport workflow it says, "we recommend to use the original counts, e.g.
txi$counts as a counts matrix, e.g. providing to
DESeqDataSetFromMatrix only takes integers, is rounding after
txi <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance="no") cts <- txi$counts cts <- round(cts) dds <- DESeqDataSetFromMatrix(cts, colData = MetaData, design = ~ ID + ... )