Stringtie/Cufflinks with yeast RNAseq

Question

[grant.hovhannisyan]

Hi Biostars,

I am working with yeast RNAseq data, and want to do guided transcriptome assembly using stringtie. Does anybody have experience with parameters of stringtie/stringtie-merge/gffcompare when working of yeast (almost no introns, short distance between genes)? For example, what are optimal values for minimum input transcript length to include in the merge, Maximum distance (range) for grouping transcript start sites, Maximum distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy?

Thanks,

[plat]

Very interested in opinions on this! I am struggling with the settings for yeast too

[grant.hovhannisyan]

Hi plat, I eventually used default parameters with stringtie, but for stringtie merge I set -g 50 to restrict the distance between the transcirpts that are merged. Plus I always was using IGV to visualize the transcripts and see whether the results were making sense.