trinity

About

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions and Availability

Module Names for trinity on philip
Machine Version Module Name
philip 2.1.0 trinity/2.1.0/INTEL-15.0.3
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Usage

Assemble RNA-Seq data:

Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU 6 --max_memory 20G 

To find out how to use these tools, type "tool -help"

For example: Trinity -help
#Required:
#
#  --seqType       :type of reads: ( fa, or fq )
#
#  --max_memory       :suggested max memory to use by Trinity where limiting can be enabled. (jellyfish, sorting, etc)
#                            provied in Gb of RAM, ie.  '--max_memory 10G'
#
#  If paired reads:
#      --left      :left reads, one or more file names (separated by commas, no spaces)
#      --right     :right reads, one or more file names (separated by commas, no spaces)
#
#  Or, if unpaired reads:
#      --single    :single reads, one or more file names, comma-delimited (note, if single file contains pairs, can use flag: --run_as_paired )

	

Resources

Last modified: May 03 2016 07:49:54.