merge transcripts id from results trinity

Question

[yaghoub.amraei]

Hi all,

how can i merge trinscript id from results de novo assembly with trinity . i have givie correlation between Transcript and LncRNA and result too much. so i have remove same isoforms with R. thanks alot

Var1                        Var2                            Freq
TRINITY_DN17567_c0_g4_i1    Ln.upTRINITY_DN1485_c0_g2_i1    -0.999347304
TRINITY_DN15020_c1_g5_i3    Ln.upTRINITY_DN1485_c0_g2_i1    0.999097516
TRINITY_DN17625_c1_g2_i3    Ln.upTRINITY_DN1485_c0_g2_i1    0.999694545
TRINITY_DN16640_c0_g1_i13   Ln.upTRINITY_DN1485_c0_g2_i1    0.999365559
TRINITY_DN10482_c0_g1_i5    Ln.upTRINITY_DN1485_c0_g2_i1    0.999155939
TRINITY_DN19436_c2_g2_i6    Ln.upTRINITY_DN1454_c0_g1_i1    0.999910259
TRINITY_DN20207_c2_g1_i6    Ln.upTRINITY_DN1454_c0_g1_i1    0.999918395
TRINITY_DN17517_c0_g9_i1    Ln.upTRINITY_DN1454_c0_g1_i1    0.999876373

Answer 1

[h.mon]

Trinity provides a script that implements the SuperTranscripts method to collapse all isoforms into one "gene", the script is:

$TRINITY_HOME/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py

The help page of this script briefly explains the method and contains references to the original paper:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/SuperTranscripts

[yaghoub.amraei]

thanks .. how can i perform from R or Excel...