REAT transcriptome

1 Run reat transcriptome on Arabidopsis illumina short read and PacBio IsoSeq

reat --jar_cromwell Inputs/Configs/cromwell.jar --runtime_configuration Inputs/Configs/cromwell_noserver_local.conf --workflow_options_file Inputs/Configs/options.json --computational_resources Inputs/Configs/compute_inputs.json transcriptome --csv_long_samples ./csv_long_sample.csv --csv_paired_samples ./csv_paired_samples.csv --all_scoring_file Inputs/Configs/plant_update.yaml --all_extra_config Inputs/Configs/external_plants.yaml --long_scoring_file Inputs/Configs/plant_update.yaml --long_extra_config Inputs/Configs/external_plants.yaml --homology_proteins Inputs/Homology/selected_species.fa --short_reads_aligner hisat --HQ_aligner minimap2 --min_identity 95 --min_intron_len 20 --max_intron_len 50000 --HQ_min_coverage 90 --HQ_min_identity 95 --skip_mikado_long --reference Inputs/Reference/Athaliana_447_TAIR10_Chr3_clean.fa > log.out 2> log.err &