Skip to content

a shell script automazing the flow of hisat2-build, hisat2-align-s, picard & cufflinks

Notifications You must be signed in to change notification settings

huangjj27/auto-hisat2

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

2 Commits
 
 
 
 
 
 

Repository files navigation

a shell script automazing the flow of hisat2-build, hisat2-align-s, picard & cufflinks

Usage

  1. unify the files as follow:
current_dir
  |-- data
        |-- genome.fna.gz    # the genome file
        |-- samples       # all the RNA samples, sperated into directories
              |-- one_of_your_sample
                    |-- R1.fastq.gz
                    |-- R2.fastq.gz
  |-- results     # separated by your sample
  1. give the script execution permission:
chmod u+x auto-hisat2.sh
  1. set the right param and run. for example:
HISAT2_DIR=/path/to/hisat2-2.1.0 \
PICARD_JAR=/path/to/picard.jar \
CUFFLINKS=/path/to/cufflinks \
GENOME=genome_name \
THREADS=max_threads \
./auto-hisat2.sh
  1. check output in results' logs or error in .errs

About

a shell script automazing the flow of hisat2-build, hisat2-align-s, picard & cufflinks

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages