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Espresso quantification without identification #18

Closed zzare-umd closed 1 year ago

zzare-umd commented 1 year ago

Hi,

I wanted to run the Espresso for just quantification with a given annotation without any identification, but I don't know if this is possible or not. I follow the steps that is expressed in the "Basic Usage" section, but the output contains the novel transcripts from espresso. Is there any way I can run only the quantification mode of the espresso?

EricKutschera commented 1 year ago

From the README: https://github.com/Xinglab/espresso/tree/v1.3.1

perl ESPRESSO_S.pl --help

[...]

-R, --read_ratio_cutoff
      min perfect read ratio for denovo detected candidate splice junctions:
      Set this as 1 for completely GTF-dependent processing (default: 0)

The description says 1 is high enough, but actually the check is >= the cutoff so the cutoff has to be more than 1 to make the check always fail. If you add --read_ratio_cutoff 2 when you run the S step and also add --read_ratio_cutoff 2 when you run the Q step then ESPRESSO should only consider annotated isoforms