Entering edit mode
Hi,
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$counts
as a counts matrix, e.g. providing to DESeqDataSetFromMatrix
". As DESeqDataSetFromMatrix
only takes integers, is rounding after txi$counts
appropriate?
txi <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance="no") cts <- txi$counts cts <- round(cts) dds <- DESeqDataSetFromMatrix(cts, colData = MetaData, design = ~ ID + ... )
Thanks!