Counts output from rpvg

[lsoldini]

Dear Patcher-lab,

I have used some pantranscriptomics tool to map RNA-seq reads on a pangenome graph, from this paper and that github.

The final output I have is a table giving read counts, effective length, as well as other features :

target_id  length   eff_length  ReadCounts  tpm
transcript_1    1012    536.576 359.436 26.4885
transcript_2    416 146.094 21  5.684
transcript_3    1353    1017.84 0   0
...

For some reasons, I could not use kallisto on my data, and I rather had to use the aforementionned tools. I am now wondering whether I could still use sleuth on the output I have.

In particular

1) Do you so any strong reason to not try using sleuth on those outputs?

2) I think I would have to transform my read counts into estimated read counts similar to the ones given by kallisto - is there anyway to do this with the info I have ?

Thank you for reading me.

Edit: there were errors in the table I have; the output is in Read Count and not estimated counts (else I could directly use sleuth).