https://github.com/hernanmd/hisat2_bovine

Scripts to index and align Bovine genome with HISAT2
https://github.com/hernanmd/hisat2_bovine

bash bioinformatics featurecounts genome genome-alignment gff3 hisat2

Last synced: about 1 month ago
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Scripts to index and align Bovine genome with HISAT2

• Host: GitHub
• URL: https://github.com/hernanmd/hisat2_bovine
• Owner: hernanmd
• License: mit
• Created: 2018-02-27T22:55:36.000Z (almost 7 years ago)
• Default Branch: master
• Last Pushed: 2018-05-22T16:15:13.000Z (over 6 years ago)
• Last Synced: 2024-05-01T14:12:31.149Z (8 months ago)
• Topics: bash, bioinformatics, featurecounts, genome, genome-alignment, gff3, hisat2
• Language: Shell
• Size: 13.3 MB
• Stars: 1
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Description

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

# Details

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

## make_bgumd31.sh

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

## run_Hisat2.sh

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

## install_ReSeQC.sh

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.

## fix_gtfFields.sh

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.