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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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UTR extension #283

Open francicco opened 4 years ago

francicco commented 4 years ago

Hi,

I'm using StrinTie in combination with braker and Trinity to annotate a genome. The idea is to recover not predicted loci but also correcting the predicted ones by for example extending their UTR regions.

UTRs

In this example both reads and the de novo (trinity in red) mapping clearly indicate UTR regions, but StringTie was not able to generate them. Why is this happening?

This is the command line I'm using:

stringtie $SPECIES.RNAonAnn.${ALIGNER}.$lib.Aligned.sortedByCoord.out.bam -l $STRINGTIELABEL \
                                -o $STRINGTIELABEL.stringtie.out.gtf -p $THREADS -A $STRINGTIELABEL.gene_abund.out \
                                -m 500 -fr -B -G augustus.Ref.$AUGREFSPECIES.ValidBraker.stringtie.gff \
                                -C $STRINGTIELABEL.stringtie.cov

Thanks a lot Francesco