Trinity

Trinity

Install

Prerequisite

sudo apt install cmake
sudo apt-get install autoconf

• Rlease page

If you come with the error below as making, try the full package. (See resolution at GitHub issue)

Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && make
make[1]: Entering directory '/home/ken/Bio/trinityrnaseq/Inchworm'
make[1]: *** No targets specified and no makefile found.  Stop.
make[1]: Leaving directory '/home/ken/Bio/trinityrnaseq/Inchworm'
make: *** [Makefile:32: inchworm_target] Error 2

cd trinityrnaseq*
make
make test_all

conda install

conda install trinity
conda install samtools bowtie bowtie2 bowtie rsem

Troubleshoot

jellyfish

Error, cannot find jellyfish installed on this system. Be sure to install it. You can get it here: http://www.genome.umd.edu/jellyfish.html at /home/ken/Bio/trinityrnaseq-v2.11.0/Trinity line 3935.

sudo apt install jellyfish

Salmon

Trinity Trinity-v2.11.0 requires salmon to be installed.  Get it here: https://combine-lab.github.io/salmon/  at /home/ken/Bio/trinityrnaseq-v2.11.0/Trinity line 3973.

sudo apt install salmon

Quick start

~/Biosoft/trinityrnaseq-Trinity-v2.5.1/Trinity --seqType fq  --max_memory 50G  --single(--samples_file)  --CPU 8  --full_cleanup
~/Biosoft/trinityrnaseq-Trinity-v2.5.1/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix MA-all-t0.01.matrix --method edgeR --samples sample

Downstream Analysis

Prerequisites

BiocManager::install('edgeR')
BiocManager::install('limma')
BiocManager::install("qvalue")
BiocManager::install('DESeq2')
BiocManager::install('ctc')
BiocManager::install("Biobase")
install.packages('gplots')
install.packages('ape')
install.packages("fastcluster")

Non-repeats Experiment (edgeR)

~/Biosoft/trinityrnaseq-Trinity-v2.8.4/Analysis/DifferentialExpression/run_DE_analysis.pl  --matrix Intest.table  --method edgeR  --dispersion 0.1

Beware that It can recognize tab-separated matrix only. if your count or expression matrix was coma-separated, your can run sed -i s/,/\t/g ${your matrix file} to change the separates.

After waiting, you are supposed have an edger{*}.dir directory and all DEGs among each groups are stored in it.

Volcano Plot and Heatmap

After you finished with run_DE_analysis.pl process, cd edger{*}.dir and run codes below with your own args.

~/Biosoft/trinityrnaseq-Trinity-v2.8.4/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix -P 1e-3 -C 2

Sample file

##      --samples_file          tab-delimited text file indicating biological replicate relationships.
##                                   ex.
##                                        cond_A    cond_A_rep1    A_rep1_left.fq    A_rep1_right.fq
##                                        cond_A    cond_A_rep2    A_rep2_left.fq    A_rep2_right.fq
##                                        cond_B    cond_B_rep1    B_rep1_left.fq    B_rep1_right.fq
##                                        cond_B    cond_B_rep2    B_rep2_left.fq    B_rep2_right.fq

Group file

If you have the sample file, you can use the sample file as the group file since the first two columns are the same

#  --samples       tab-delimited text file indicating biological replicate relationships.
#                                   ex.
#                                        cond_A    cond_A_rep1
#                                        cond_A    cond_A_rep2
#                                        cond_B    cond_B_rep1
#                                        cond_B    cond_B_rep2

Tricks

If you don’t like the color of heatmap, you can can change the below lines in file:
$TrinityFile/Analysis/DifferentialExpression/R/heatmap.3.R

Errors

My environment:

██████████████████  ████████     ken@manjaro
██████████████████  ████████     OS: Manjaro 21.0.7 Ornara
██████████████████  ████████     Kernel: x86_64 Linux 5.4.124-1-MANJARO
██████████████████  ████████     Uptime: 5m
████████            ████████     Packages: 1678
████████  ████████  ████████     Shell: zsh 5.8
████████  ████████  ████████     Resolution: 1920x1080
████████  ████████  ████████     DE: GNOME 3.38.5
████████  ████████  ████████     WM: Mutter
████████  ████████  ████████     WM Theme: Matcha-dark-sea
████████  ████████  ████████     GTK Theme: Matcha-sea [GTK2/3]
████████  ████████  ████████     Icon Theme: Papirus-Dark-Maia
████████  ████████  ████████     Font: Noto Sans 11
████████  ████████  ████████     Disk: 769G / 1.5T (54%)
                                 CPU: Intel Xeon E3-1535M v6 @ 8x 4.2GHz [51.0°C]
                                 GPU: NVIDIA Quadro M2200
                                 RAM: 3208MiB / 64042MiB

Trinity version: trinityrnaseq-v2.12.0

Error code:

1. htslib

configure: error: cannot find required auxiliary files: config.guess config.sub
make[2]: *** [Makefile:10: htslib/version.h] Error 1
make[2]: Leaving directory '/home/ken/Bio/trinityrnaseq-v2.12.0/trinity-plugins/bamsifter'
make[1]: *** [Makefile:32: bamsifter_target] Error 2
make[1]: Leaving directory '/home/ken/Bio/trinityrnaseq-v2.12.0/trinity-plugins'
make: *** [Makefile:39: trinity_essentials] Error 2

configure: error: cannot find required auxiliary files: config.guess config.sub
This problem comes the version of autoconf (see GitHub Issue)
We can solve this by downgrade the version of autoconf. 2.69 works to me.

Install the autoconf: andyguan01_2 2019

sudo pacman -R autoconf

wget ftp://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz
tar zxvf autoconf-2.69.tar.gz
cd autoconf-2.69
./configure --prefix=/usr/
make && make install