Information & Computational Sciences

Tablet Frequently Asked Questions

Tablet only seems to be using up to 1GB of memory even though I have much more than that installed on my PC

Due to the way the Java runtime works, we have developed Tablet to run with a maximum memory allocation of 1GB (32 bit version) or 4GB (64 bit version). This is described in more detail in the Allocating Memory help topic, along with instructions on how to adjust (higher or lower) the amount of memory Tablet will use.

Maq assemblies do not appear to be loading. Which Maq files does Tablet require?

The Maq files that Tablet expects are the text file which can be generated from the .map file and the fastq file which can be generated from the .cns maq file (see the
Maq Reference Manual for more details).

To produce the text file from the .map file, you should execute the mapview command. The format of the command should resemble maq mapview > output.txt.

To produce the fastq file from the .cns file, you should execute the cns2fq command. The format of the command should resemble maq cns2fq input.cns > output.fastq.

Also see our Assembly Conversion guide that covers coverting between several common assembly formats.

Why does every contig in my BAM assembly show the number of reads as “?”?

BAM assemblies are treated differently to other file formats in Tablet (to allow instant access to portions of very large assemblies) and because of this it means that Tablet is not able to provide summary information simply because Tablet hasn’t yet read all of the contig (and it most cases it never will). Once you view a contig, information on the region you view will become available, but please be aware that the numbers you see will change as you move around the contig using the BAM controls. See BAM Data Visualization for more information.

Updated Tablet can now provide this information so long as the BAM’s index file was generated with samtools 0.1.8 or later.

What are the “CIGAR-I” features that Tablet adds to SAM and BAM files?

Tablet automatically adds these features types for column positions where an insertion into the reference has occurred (and has been marked up in the CIGAR formatting of the original SAM or BAM file). If you hover the mouse over the feature in the Features Table, then a tooltip will appear that also informs you how many reads at that position were tagged in this way.

How do I run more than one instance of Tablet on OS X?

You can start the first instance using the normal shortcut. Any additional copies can be started by using the Terminal and typing

  open -n /Applications/

What command line options does Tablet support?

Tablet supports several command line options. They are detailed in the Command Line Options section of the online help.

How do I run the maqtoace program when using OS X?

A launcher for maqtoace isn’t distributed with Tablet for OS X due to the way the Apple package format works. However, you can manually start the program by
opening a Terminal window, and typing:

  cd /Applications/
  java -Xmx1024m -cp tablet.jar

Does Tablet support launching via Java Web Start?

Yes. Tablet can be run via Java Web Start (Java 7 required) by visiting

This will launch Tablet with its default settings, allocating 1024MB of memory for use. You can change this setting by including the argument


You can also pass it files to open (assuming they’re located on a web server somewhere), for example


If you need two files (eg reference and assembly), then it would be


You can combine all of the above too. The order doesn’t matter – just separate arguments with &.