rnaspades

Where:

Run rnaspades in the same folder as your RNA-seq reads. (Use File --> OpenDir to open a new window in your reads folder.)

Input:

RNAseq reads: Before opening this menu, select RNA readfiles. For paired-end reads rnaspades,  works with pairs of files. Files can be selected in pairs using File --> guesspairs.py.


Output:
The default "../reads.trimmed.corrected.rnaspades" means that output files will be written to a folder in the parent folder (..)  called rnaspades.

The most useful human-readable output files:

rnaspades.log - Detailed progress on the assembly.