The File Menu

Read An Entry ...

Read an entry for this sequence, but keep it separate from the others. See the section called The "Entry" in Chapter 1 to see what we mean when we say "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).

This function only reads the feature section of the input file - the sequence (if any) is ignored.

ACT can read these feature files formats:

Save Entry

Save the 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, ACT will prompt the user for a new name.

Save All

Save all the entries that have been loaded on top of this sequence.

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).

Read BAM / VCF ...

ACT can read in and visualise BAM, VCF and BCF files. These files need to be indexed as described below. They require ACT to be run with at least Java 1.6.

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 ACT, 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.

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 (yellow), 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).

Edit In Artemis ...

Open an Artemis edit window for this sequence and features. All changes made in the Artemis window will be immediately visible in the ACT window and vice versa.

See the Artemis manual for more about Artemis.

Close

Close this window.