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Stringtie/Cufflinks with yeast RNAseq

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,

rna-seq stringtie cufflinks gffcompare cuffcompare
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written by grant.hovhannisyan grant.hovhannisyan

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

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written by plat plat

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.

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written by grant.hovhannisyan grant.hovhannisyan

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