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: 9 months 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 (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-05-22T16:15:13.000Z (over 7 years ago)
- Last Synced: 2025-01-03T21:42:29.845Z (11 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.