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Building a Custom CTAT Genome Lib

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Brian Haas edited this page Mar 27, 2019 · 1 revision

Building a Custom CTAT Genome Lib

To build a custom FusionFilter dataset (CTAT genome lib), you require a genome in FASTA format (eg. 'genome.fa') and a gene annotation set in GTF format (eg. transcripts.GTF).

You will also need the following tools installed and available via your PATH setting.

And download the Pfam-A.hmm database, and prepare it for Pfam searches with hmmer:

 Building the Pfam-A database involves the following.
 % gunzip Pfam-A.hmm.gz
 % hmmpress Pfam-A.hmm

After having the above tools and database installed, the steps to build a CTAT genome lib include:

  1. (Optional) Remove any transcripts from your transcripts.GTF file that you do not want included as candidate fusion targets.

  2. Run the CTAT genome builder like so:

    ${ctat-genome-lib-builder-basedir}/prep_genome_lib.pl
    --genome_fa genome.fa
    --gtf transcripts.gtf
    --pfam_db /path/to/Pfam-A.hmm
    --CPU 10 # number of threads

      (and optionally) 
 --fusion_annot_lib /path/to/file/containing/fusion_annotations.txt  # see below

Executing the above will generate and populate the CTAT genome lib, by default called 'ctat_genome_lib_build_dir' in your current working directory. See the additional options available to prep_genome_lib.pl above for further customization.

Optional, include Fusion annotations

If you would like to include annotations for known fusions, create a file containing the format:

 geneA--geneB(tab)some annotation text that describes this fusion
 ...

and you can also include individual gene annotations like so:

 geneA(tab)any annotation I want to include for this gene symbol
 ...

For example:

    ATIC--ALK       Cosmic{samples=99,mutations=12,papers=20},chimerdb_pubmed{Anaplastic large cell lymphoma (ALCL),Inflammatory myofibroblastic tumour}
    ATL2--HNRPLL    YOSHIHARA_TCGA_num_samples[BRCA:1|LUAD:1],{Klijn_CCL:Lung=1}
    ATM     ATM_serine/threonine_kinase,ArcherDX_panel,FoundationOne_panel
    ATL1    atlastin_GTPase_1
    ATL2    atlastin_GTPase_2
    ATL3    atlastin_GTPase_3

In case you're curious about any data formatting issues or required contents, please see examples for data sets we provide source data files and fully built CTAT genome libs at https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/

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