Where:
Run stringetie in the same folder as your .bam files. (Use File --> OpenDir to open a new window in
your RNA-seq reads folder.)
Input:
bamfiles: Before opening this menu, select files with the
.bam extension to be matched
to the merged
transcriptome.
Merged
transcriptome (.gtf) - This is the transcriptome created by stringtie-merge.
It should be in the gtffiles folder.
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:
New .gtf files will
be written to the output folder
eg. ballgown.
These .gtf files will
contain the gene
annotation from the merged transcriptome, plus estimates of gene
expression levels, for further analysis using software such as the BioConductor R package.