File | Description |
|---|---|
Top-level folder files | |
*.Pjt | This is the file that is loaded in the NextGENe Viewer when the project is complete to allow review of the analysis results. |
_Parameters.txt | This file contains information about the settings that were used for the project. If condensation was carried out as preliminary step and then alignment was carried out as part of the same project, then a _Parameters.txt file is created that contains the settings for all the project steps. |
_StatInfo.txt | This file provides basic information and various statistics about the assembly process. • Basic information: • The general steps that were used • Process times • Sample file names and output file names • Statistical information: • The respective counts for matched and unmatched reads • Average read length • Coverage • Total number of covered bases for the reference • The username for the user who ran the analysis if User Management is turned on Note: The average coverage is calculated according to the following (which therefore excludes zero coverage regions): (No. of aligned bases)/(Total no. of covered bases) |
unmatched.fasta unmatched.csfasta | This file contains all the reads that did not match to the reference file. You can use this file further analysis of your samples. |
Paired Data output only | |
_Arranged.fasta _Arranged.csfasta | When carrying out a paired read analysis, NextGENe first scans the sample files to determine if the reads are arranged in the files. If the reads are arranged, then no arranged files are created; otherwise, NextGENe arranges the sample files so that the paired reads are in a similar order in both files, and then saves these arranged reads in an arranged file in either a .fasta format or a csfasta format. Going forward, you can use these arranged files for analysis. Note: The Sequence Operation Tool contains an option for arranging paired read sample files. If you use this option to arrange the reads in your sample files before you carry out the alignment, then NextGENe skips the step of arranging the sample files. See The NextGENe Sequence Operation Tool. |