Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simple two-column map file of transcript-to-gene-ID. This gives me an output like this for each fastq:
Name Length EffectiveLength TPM NumReads ENSMUSG00000114165 2016 1815.57 0.0732938 3.29409
I tried simply passing these outputs on as input to DESeq2 for differential expression, selecting under input "TPM values (e.g. from sailfish or salmon)", then for Gene mapping format selecting "Transcript-ID and Gene-ID mapping file" and specifying the same two-column table used for the salmon runs (haha).
I got this vague error:
Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 6 elements Calls: read.table -> scan
So, not sure where the problem's arising, but for starters, the salmon output contains both TPM and NumReads (i.e., I presume, a read count estimate). Do I need to extract one or the other of these columns to pass on to DESeq2? And also, is the transcript-to-gene map even necessary for DESeq2 since the gene-level summary has already been done by salmon?
Thanks so much for your help!