If you are following the RNA-Seq reference-guided workflow (i.e., if you chose Transcriptome/RNA-Seq Assembly in the Choose Assembly Workflow screen, and Reference-guided assembly in the Choose Assembly Type screen), output results are saved in an .assembly package folder labeled with the user-specified project name and the suffix _RNA-Seq. This folder contains the following files:

Subfolder Name File Name Description
[project name].astar An ArrayStar project file containing data from all of the samples.
[project name].script The main script for a reference-guided assembly project. It can be rerun from the Begin Project screen by selecting Re-run Local Assembly.
[project name].table.txt The table containing project descriptions and corresponding files; used by the main script.
[project name].template.script The reference-guided workflow script, which is applied to all projects listed in .table.txt.
[project name].astar.script The script file executed by ArrayStar when the Launch in ArrayStar button is pressed in the Project Report.
query‘n’.script The script containing query sequences. This script is generated only if a multiple project assembly includes groups that contain non-equal numbers of files.
_tableScript.template.script The script template, executed by the XNG assembler in order to run the QNG assembler. This script is not present before the run and is generated by XNG.
[project name]-qng.script After SeqMan NGen finishes running the XNG part of the assembly, QNG assembly is performed using this script. In multi-sample projects, this file references .table.txt.
[project name].Results.txt A tab-separated table showing the assembly results.
Sample‘n’.assembly sample‘n’-0.isoforms-features Each .assembly project contains a set of files relating to a single contig.
sample‘n’-0.genes-features
sample‘n’-0.bam
sample‘n’-0.coverage
Sample’n’-Reports ‘n’-0.report.txt A summary of the run; also shown in the Project Report.

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