Help importing data

[Katrin Moller]

Hi there, 

I have a dataset produced by Nanopore sequencing. Due to my lack of knowledge in processing this, I took advantage of the workflow packages that Nanopore provides, via Epi2meLabs: https://github.com/epi2me-labs/wf-transcriptomes 

This pipeline processed the data, identifies transcripts using StringTie and counts them using Salmon. It then concatenates them into one file, which includes the transcript ID and then the relevant transcript counts for all the different samples as columns. 

Looks like this:

Reference km12_8_NPC km12_8_Day2 km13_5_Day2 km13_5_NPC km09_1_Day2 km09_1_NPC
ENSMUST00000177163.8 138487.0 73335.0 76820.0 109797.0 58926.0 82626.0
ENSMUST00000176010.8 134414.0 71147.0 74860.0 106470.0 57575.0 80039.0
ENSMUST00000176683.8 134301.0 71055.0 74802.0 106359.0 57512.0 79962.0

Unfortunately, the pipeline does not spit out the typical quant.sf file that you would expect from Salmon.

I realize this is not the typical dataset used by IsoformSwitchAnalyzeR, but is there anyway to import this dataset using importIsoformExpression() ? 

I tried already:
salmonQuant <- importIsoformExpression(
  sampleVector="NPC-Day2_results/de_analysis/de_transcript_counts.tsv")

but got the error:

Error in importIsoformExpression(sampleVector = "NPC-Day2_results/de_analysis/de_transcript_counts.tsv") : Some of the files pointed to are not quantification files from Kallisto/Salmon/RSEM/StringTie. They did no contain the column names typically generated by Kallisto/Salmon/RSEM/StringTie. Are you sure it is the right files?

Would love to hear if this table is usable or not.