Question: merge transcripts id from results trinity
1
gravatar for yaghoub.amraei
6 months ago by
yaghoub.amraei10 wrote:

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
trinity rna-seq R • 319 views
ADD COMMENTlink modified 6 months ago by h.mon27k • written 6 months ago by yaghoub.amraei10
2
gravatar for h.mon
6 months ago by
h.mon27k
Brazil
h.mon27k wrote:

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 top the original paper:

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

ADD COMMENTlink written 6 months ago by h.mon27k

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

ADD REPLYlink written 6 months ago by yaghoub.amraei10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1555 users visited in the last hour