stringtie to ballgown

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.