New GeneMarkerHTS project caveats
Before you add a new project in GeneMarkerHTS, it is important to note the following:
• Every GeneMarkerHTS project is named project.pjt, and the project file as well as all the project output files are saved in a folder that, by default, is named as:
<project creation date>T<project run time_v<GeneMarkerHTS version>+<f<n>).ci
where:
• The date is in the following format: year_month_day.
• The time is in 24-hour time.
• The software version is three digit showing the major release, the minor release, and the point release.
• f<n> is developer-specific information that is used for debugging purposes.
For example, a project folder named 2023_09_12_T14-28_v2.6.0+ f07776306.ci indicates a project that was run on October 09, 2023 at 2:18 pm in the afternoon using version 2.0.6 of GeneMarkerHTS. This default naming convention allows you to save multiple projects in the same folder without overwriting an existing project.
• If you do not specify a folder in which to save the project, then GeneMarkerHTS informs you that the project folder was not set, and asks you if you want to use the default project folder, which is the folder that contains the project sample files.
• The default reference that is supplied in GeneMarkerHTS is the revised Cambridge Reference Sequence (rCRS). If you select a different reference, then it must be in either FASTA or GBK format.
• When you add a new project in GeneMarkerHTS, the sample files that you load must be in one of three formats: compressed FASTQ files (fastq.qz), uncompressed FASTQ files (.fastq), or BAM files (.BAM).
• The Name of each sample file and the names of all the corresponding output files for a project are automatically generated from the names of the added sample files. You can edit the Name for a sample file.
• GeneMarkerHTS automatically groups paired reads in a sample, but you can split a group of paired reads into individual samples.
• GeneMarkerHTS automatically adjusts the default values for both Identity and Soft Clipping based on the sequencer that you select. If you change the value for either one or both settings, then GeneMarkerHTS automatically selects “Other” for Sequencer, and you cannot select a different Sequencer value.
• Filter settings and table settings control the criteria for variant calling and for displaying project information in the Variants table in the Mito Alignment Viewer. Filter settings determine the alleles that are called for a project in the STR Analysis Viewer. You can adjust filter settings and table settings before or after alignment of the samples in a project.
• Amplicon settings define the amplicon-sequenced regions that were used for the mtDNA alignment project. You can adjust amplicon settings only before the alignment of the samples in a project.
• PHI settings control which personal health information to mask for a subject. You can adjust PHI settings only before the alignment of the samples in a project.