What is trinity test ?
Download and Install Triniy
Source code : https://github.com/trinityrnaseq/trinityrnaseq
Dowload latest Trinity release : https://github.com/trinityrnaseq/trinityrnaseq/releases (latest version : Trinity-v2.3.2)
$ make <===> This should build Inchworm and Chrysalis, both written in C++
$ make plugins <===> This will build the additional plugin components that provide support for downstream analyses
Additional tools required for running Trinity include:
$ sudo apt-get install bowtie2
To test your installation of Trinity, try assembling the small sample data set provided with Trinity like so:
cd sample_data/test_Trinity_Assembly/
./runMe.sh
sample_trinity_test.png
The parameter about trinity
Run "./Trinity --help" to see the parameters about trinity . If you wants to know more parameters , please run "./Trinity --show_full_usage_info" to check them .
| Parameter | Description |
|---|---|
| Required parameters : | You need add the blow parameters when run trinity testing . |
| --seqType <string> | type of reads: ('fa' or 'fq') |
| --max_memory <string> | suggested max memory to use by Trinity where limiting can be enabled. eg: --max_memory 16G |
| --left <string> | left reads, one or more file names (separated by commas, no spaces) |
| --right <string> | right reads, one or more file names (separated by commas, no spaces) |
| Optional parameters : | |
| --version | check version |
| --verbose | provide additional job status info during the run. |
| --CPU <int> | number of CPUs to use, default is 2 |
| --output <string> | name of directory for output (will be created if it doesn't already exist) |
| --SS_lib_type <string> | Strand-specific RNA-Seq read orientation. If paired RF or FR,if single F or R. eg : -- SS_lib_type RF |
| --min_contig_length <int> | minimum assembled contig length to report, default is 200 |
| --long_reads <string> | fasta file containing error-corrected or circular consensus (CCS) pac bio reads |
| --genome_guided_bam <string> | genome guided mode, provide path to coordinate-sorted bam file. (see genome-guided param section under --show_full_usage_info) |
| --full_cleanup | only retain the Trinity fasta file, rename as ${output_dir}.Trinity.fasta |
| --trimmomatic | run Trimmomatic to quality trim reads see '--quality_trimming_params' under full usage info for tailored settings. |
| --show_full_usage_info | show the many many more options available parameters for running Trinity |
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