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Published 20 hours ago • verified publisher icon NBISweden

TranscriptAssembly pipeline can be improve

Open Juke34 opened this issue 5 years ago • 1 comments

Should be more generalized. With choice for read aligner:

  • star
  • Hisat2

choice of different assemblers (Why? Because better result: ):

  • denovo:
    • soap denovo trans
    • Oases
    • trinity
  • guided
    • Stringtie
    • Scallop
    • Bayerassembler

And an optional filtering step at the end: Mikado
EviGene

Juke34 avatar Jan 31 '20 11:01 Juke34

we could also add normalization (as an option if data too big). do we do denovo or reference guided with trinity? (we could do both) need QC (transcript QC : detonate, transrate, more?) need filtering maybe

use scilifelab (nf-core) RNAseq pipeline? to check

LucileSol avatar May 26 '21 11:05 LucileSol