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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Use of StringTie to assemby of unannotated intron retention transcripts #409

Open CBenetti opened 9 months ago

CBenetti commented 9 months ago

The aim is to be able to obtain the full transcript sequence in case of unannotated intron retention events. Following the StringTie workflow, this would mean considering retained introns (which have been previously identified with IRFinder) as potential new exons, as to reconstruct the full transcript and quantify them trough the classical pipeline, while still being able to use existing annotations. A) The question is: is there an existing setting which I could implement to obtain such result, or is it something I should costumize? B) If it isn't an existing feature of StringTie, could the following be a solution:

  1. When generating BAM files, adding in STAR splice junctions corresponding to the exon-intron junction as to generate XS tags for those reads spanning the exon - intron junction for both files
  2. Add to gtf annotation file coordinates of retained introns and gene of appartenece
  3. Running StringTie with custom annotations and custom BAM files

Thank you in advance

CuteGold0407 commented 2 months ago

hi,have you solved this issue?