Full-length transcript prediction using nanopore sequencing

Pipeline for transcript prediction of the chicken genome using nanopore sequencing technology

Data preparation

To run this pipeline, following files should be prepared:

1. Reference genome:
   • fasta: Gallus_gallus.GRCg6a.dna_sm.toplevel.fa
   • gtf: Gallus_gallus.GRCg6a.102.gtf
2. Fastq files:
   • tissue_sampleid.fq.gz

Configuration file

  * Chicken_Kidney_CD.fq
  * Chicken_Ovary_CC.fq

N.B. The file can not be compressed, otherwise NanoPlot would report errors

Running the pipeline

sbatch nanopore_ann_run.sh

N.B. The pipeline is currently configured on UC DAVIS FARM server, which will be updated in the future.