Scripts to index and align Bovine genome with HISAT2

The scripts in this repository enables to index and align a Bovine NGS dataset with the UMD3.1.1 Bovine Genome

Before running, please open the scripts and customize for the amount of cores (threads) in your platform.

Use the script to index the UMD3.1.1 Bovine Genome with the HISAT2 software.

Use the script to map the cleaned reads with the genome index built from the previous script.

Use the script if installing ReSeQC in the officially documented way does not work. The script assumes nothing about the target destination, except being a Debian-compatible Linux distribution. It requires root privilege to install dependencies.

Use this script if running featureCounts results in the following message:

Warning: failed to find the gene identifier attribute in the 9th column of the provided GTF file. The specified gene identifier attribute is 'gene_id' The attributes included in your GTF annotation are 'transcript_id "rna...";'

The script removes all rows without the gene_id annotation in the last field of a GTF record.