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TranscriptAssembly pipeline can be improve #3

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Juke34 opened this issue Jan 31, 2020 · 1 comment
Open

TranscriptAssembly pipeline can be improve #3

Juke34 opened this issue Jan 31, 2020 · 1 comment
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enhancement New feature or request Provide example code Provide an example of code, with data input, output, and other parameters Provide test data A minimal test data should be provided with the request

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@Juke34
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Juke34 commented Jan 31, 2020 •
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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
@mahesh-panchal mahesh-panchal added enhancement New feature or request Provide example code Provide an example of code, with data input, output, and other parameters Provide test data A minimal test data should be provided with the request labels Feb 3, 2020
@LucileSol
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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

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enhancement New feature or request Provide example code Provide an example of code, with data input, output, and other parameters Provide test data A minimal test data should be provided with the request
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@Juke34 @mahesh-panchal @LucileSol