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A Trix index consists of a pair of files that allow for fast look-up of free text associated with a
list of identifiers. The index is created from a single line-oriented text file using the program
ixIxx
. Each line in the text file starts with an identifier, followed by free text
associated with the ID. For a more complete description of how to make a searchable track hub (or
custom track), please visit the Quick Start
Guide to Searchable track hubs.
To complete the steps below you must first download the ixIxx
utility. For more
information on downloading our command line utilities, see these
instructions.
To create a Trix index, follow these steps:
id1 this is text for id1
id2 this is text for id2
id3 this is text for id3
ixIxx
program on your text file. ixIxx input.txt myTrix.ix myTrix.ixx
SIRT1, BRCA1, TP53
in the fourth name
column, and you built the bigBed using the option of
-extraIndex=name
to index the name field you can create an
input.txt such as the following that associates the bigBed name with other
identifiers people might search for or with shorter spellings of the names:
SIRT1 sirt1 sir sirt SIR SIRT Sirtuin SIR2-Like ENSG00000096717 NM_012238 BRCA1 brca1 brca brc BRC BRCA breast cancer 1 ENSG00000012048 NM_007300 TP53 tp53 tp5 TP5 Tumor Protein P53 ENSG00000141510 NM_001126112
ixIxx
program on your text file,
taking into account the length of your longest word. ixIxx input.txt myTrix.ix myTrix.ixx
The ixIxx
utility has a default of 31 characters for words. If you build an input.txt
with longer words, such as very long accessions, you neeed to add the option -maxWordLength=N
to override the default and expand it to the size you are using for the longest words in your index.
If you want to use your Trix index in a track hub, see the searchTrix
setting in the
Track Database Definition Document.
Review our Quick Start Guide to Searchable track hubs for illustrated steps building a track hub.
There are also tools available for taking genePred format to trix format, such as this gpToIx.pl perl script.