Where:
Run stringtie in the same folder as your bam files. When hisat2
completes, you should already have a blreads window in the
bamfiles folder.
Input:
bamfiles: Before opening this menu, select files with the
.bam extension to be mapped to the features in the genome. For every pair of read files processed by hisat,
there will be a single bam file.
Reference transcriptome (.gtf) - This is the transcriptome
(set of mRNAs) corresponding to the genes in the genome. The file
should probably be in the same directory as the genome file.
Name prefix - This will be added to the name of every gene
transcript in the output, so it should be short. For example, a
descriptive prefix for transcripts from Rhodosporidium
diobovatum, might be Rdio.
Output:
The default "../gtffiles" means that output files will be written
to a folder in the parent folder (..) called gtffiles.