reference for this pipeline

[mlpy18]

hi, eric.
Does the version of genome and transcipts gtf affect the results when we run the pipeline, which version would be better , we use GRCh38.p14.genome.fa and gencode.v45.chr_patch_hapl_scaff.annotation.gtf, but some of the novel transcipts we identified can not verified in NGS data. Thank you very much.

[EricKutschera]

The choice of reference files can change the output. I usually use the latest GENCODE primary assembly files:
https://github.com/Xinglab/espresso/blob/v1.5.0/snakemake/snakemake_config.yaml#L58

ESPRESSO needs the same reference version that was used to align the reads in order to match up coordinates