hisat2

Where:

Run hisat2 in the same folder as your RNA-seq reads. (Use File --> OpenDir to open a new window in your RNA-seq reads folder.)

Input:

RNAseq reads: Before opening this menu, select RNA-seq readfiles to be mapped to the genome. For paired-end reads, hisat2 words with pair of files. Files can be selected in pairs using File --> guesspairs.py.

Choose any genome index file (eg. .ht2) - Choose any of the .ht2 files created by hisat2-build. All .ht2 files that begin with the same basename will be used for mapping your reads to the genome.

Output:
The default "../bamfiles" means that output files will be written to a folder in the parent folder (..)  called bamfiles.

For every pair of read files in the input, there will be a single bam file.