search

Xinglab / espresso

Other
58 stars 4 forks source link

reference for this pipeline #69

Open mlpy18 opened 3 months ago

mlpy18 commented 3 months ago

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 commented 3 months ago

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