The File Menu

Most of the items in this menu are used to read and write entries and parts of entries, the exceptions are Clone and Close.

Show File Manager ...

This will open the file manager, or if it is already open will bring it to the foreground. Entries can be dragged from the file manager into the artemis main window and dropped. When dropped the entry is then read in and displayed.

Read An Entry ...

Read an entry (see the section called The "Entry" in Chapter 1), but keep it separate from the others. A new button will be created on the entry button line for the new entry. The new entry will be marked as active (see the section called The Active Entries in Chapter 1) and will be the new default entry (see the section called The Default Entry in Chapter 1).

See the section called Sequence and Annotation File Formats in Chapter 1. This function only reads the feature section of the input file - the sequence (if any) is ignored.

Read Entry Into

Read the features from an entry (see the section called The "Entry" in Chapter 1) chosen by the user and then insert them into the entry selected by the user.

Read BAM / VCF ...

Artemis can read in and visualise BAM, VCF and BCF files. These files need to be indexed as described below. They require Artemis to be run with at least Java 1.6. Some examples can be found on the Artemis homepage.

BAM files need to be sorted and indexed using SAMtools. The index file should be in the same directory as the BAM file. This provides an integrated BamView panel in Artemis, displaying sequence alignment mappings to a reference sequence. Multiple BAM files can be loaded in from here either by selecting each file individually or by selecting a file of path names to the BAM files. The BAM files can be read from a local file system or remotely from an HTTP server.

BamView will look to match the length of the sequence in Artemis with the reference sequence lengths in the BAM file header. It will display a warning when it opens if it finds a matching reference sequence (from these lengths) and changes to displaying the reads for that. The reference sequence for the mapped reads can be changed manually in the drop down list in the toolbar at the top of the BamView.

In the case when the reference sequences are concatenated together into one (e.g. in a multiple FASTA sequence) and the sequence length matches the sum of sequence lengths given in the header of the BAM, Artemis will try to match the names (e.g. locus_tag or label) of the features (e.g. contig or chromosome) against the reference sequence names in the BAM. It will then adjust the read positions accordingly using the start position of the feature.

When open the BamView can be configured via the popup menu which is activated by clicking on the BamView panel. The 'View' menu allows the reads to be displayed in a number of views: stack, strand-stack, paired-stack, inferred size and coverage.

In Artemis the BamView display can be used to calculate the number of reads mapped to the regions covered by selected features. In addition the reads per kilobase per million mapped reads (RPKM) values for selected features can be calculated on the fly. Note this calculation can take a while to complete.

Variant Call Format (VCF) files can also be read. The VCF files need to be compressed and indexed using bgzip and tabix respectively (see the tabix manual and download page). The compressed file gets read in (e.g. file.vcf.gz) and below are the commands for generating this from a VCF file:

        bgzip file.vcf
        tabix -p vcf file.vcf.gz
        

Alternatively a Binary VCF (BCF) can be indexed with BCFtools and read into Artemis or ACT.

As with reading in multiple BAM files, it is possible to read a number of (compressed and indexed) VCF files by listing their full paths in a single file. They then get displayed in separate rows in the VCF panel.

For single base changes the colour represents the base it is being changed to, i.e. T black, G blue, A green, C red. There are options available to filter the display by the different types of variants. Right clicking on the VCF panel will display a pop-up menu in which there is a 'Filter...' menu. This opens a window with check boxes for a number of varaint types and properties that can be used to filter on. This can be used to show and hide synonymous, non-synonymous, deletion (grey), insertion (magenta), and multiple allele (orange line with a circle at the top) variants. In this window there is a check box to hide the variants that do not overlap CDS features. There is an option to mark variants that introduce stop codons (into the CDS features) with a circle in the middle of the line that represents the variant. There are also options to filter the variants by various properties such as their quality score (QUAL) or their depth across the samples (DP).

Placing the mouse over a vertical line shows an overview of the variation as a tooltip. Also right clicking over a line then gives an extra option in the pop-up menu to show the details for that variation in a separate window. There are also alternative colouring schemes. It is possible to colour the variants by whether they are synonymous or non-synonymous or by their quality score (the lower the quality the more faded the variant appears).

There is an option to provide an overview of the variant types (e.g. synonymous, non-synonymous, insertion, deletion) for selected features. Also, filtered data can be exported in VCF format, or the reconstructed DNA sequences of variants can be exported in FASTA format for selected features or regions for further analyses. These sequences can be used as input for multiple sequence alignment tools.

Save Default Entry

Save the default entry to the file it came from, unless the entry has been given a new name, in which case the entry is saved to a file with that name. If the entry has no name, Artemis will prompt the user for a new name. [shortcut key: S]

Save An Entry

This item will do the same as "Save Default Entry" for the chosen entry.

Save An Entry As

This sub-menu contains the less frequently used save functions.

New File

Ask for the name of file to save the given entry to. The name of entry (as displayed in the entry button line) will change to the new name.

EMBL Format

This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in EMBL format. Note that currently the header of a GENBANK entry can't be converted to the equivalent EMBL header (it will be discarded instead).

GENBANK Format

This does the same as "Save An Entry As -> New File ...", but will write the features and sequence of the entry in GENBANK format. Note that currently the header of a EMBL entry can't be converted to the equivalent GENBANK header (it will be discarded instead).

Sequin Table Format

This saves a file in Sequin table format which is used by Sequin.

GFF Format

Writes the features in GFF format and sequence of the entry in FASTA format to a file selected by the user. Note that if you use this function on an EMBL or GENBANK entry the header will discarded.

EMBL Submission Format

This does the same as "Save An Entry As -> EMBL Format ...", but will write an entry/tab file that contains only valid EMBL qualifiers (see the section called extra_qualifiers in Chapter 6) and valid EMBL keys (see the section called extra_keys in Chapter 6). It will also check that the start and stop codons of each CDS are sensible, that no two features have the same key and location and that all required EMBL qualifiers are present.

Save All Entries

This acts like "Save Default Entry", but save all the entries.

Write

Amino Acids Of Selected Features

Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in FASTA format.

PIR Database Of Selected Features

Prompt for a file name and then write the translation of the bases of the selected features to that file. The file is written in PIR format (similar to FASTA, but with a * as the last line of each record).

Bases Of Selection

Prompt for a file name and then write the bases of the selection to that file in the selected format. If the selection consists of features (rather than a base range) then the bases of each feature will be written to the file as a separate record. If the selection is a range of bases, then those bases will be written.

Upstream Bases Of Selection

Prompt for a number and a file name, then write that many bases upstream of each selected feature to the file in the selected format. For example if the selected feature has a location of "100..200", then asking for 50 upstream will write the bases in the range 50 to 99. Writing upstream bases of a feature on the complementary strand will work in the expected way.

Downstream Bases Of Selection

Prompt for a number and a file name, then write that many bases downstream of each selected feature to the file in the selected format.

All Bases

Prompt for a file name, then write the complete sequence to that file in the selected format.

Codon Usage of Selected Features

Prompt for a file name, then write a codon usage table for the selected features. The file in written in the same format as the data at Kazusa codon usage database site. In the output file each codon is followed by it's occurrence count (per thousand) and it's percentage occurrence. (See the section called Add Usage Plots ... to find out how to plot a usage graph).

Clone This Window

Make a new main window with the same contents as the current window. All changes in the old window will be reflected in the new window, and vice versa. The exception to this rule is the selection (see the section called The Selection in Chapter 1), which is not shared between the old and new window.

Save As Image Files (png/svg)

Print out the contents of the current window. All or some of the window panels can be selected for printing to an image file.

SVG (scalable vector graphics) is an XML based vector image format. These images can be converted to a raster image (e.g. png, tiff) at any resolution by exporting it from applications such as Inkscape (http://inkscape.org/) or gimp (http://www.gimp.org/). Therfore the SVG format can be useful for creating publication quality figures.

The other formats available (png, jpeg etc) and are raster or bitmap images.

Print

This option can be used to print the contents of the current window to a file as PostScript or to a printer.

Print Preview

This opens the print image in a preview window. This shows what the image will look like when printed to a file.

Preferences

This enables the user to define their own shortcut preferences.

Close

Close this window.