Where:
Run Trinity in the same folder as your RNA-seq reads. (Use File
--> OpenDir to open a new window in your RNA-seq reads
folder.)
Input:
RNAseq reads: Before opening this menu, select RNA-seq
readfiles to be mapped to the genome. For paired-end reads,
Trinity works with pairs of files. Files can be selected in pairs
using File --> guesspairs.py.
Trinity does not allow combining paird-end and single read data!
Before running Trinity, select ONLY paird-end, or ONLY single-end
read files.
Resources
maximum memory to use (Gb) - The Trinity Wiki FAQ suggests
setting 1Gb RAM per million reads. "The memory usage mostly depends on the
complexity of the RNA-Seq data set, specifically on the number of
unique k-mers. If you do not have access to a high-memory server,
other
freely available options are available."
Output:
The default "../reads.trimmed.corrected.Trinity" means that output
files will be written to a folder in the parent folder (..)
called Trinity.
The progress of the assembly can be found in trinity.log.