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

2. give the script execution permission:

chmod u+x auto-hisat2.sh

3. 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

4. check output in results' logs or error in .errs