GFK: Genomon-fusion for K computer                   

Copyright (c) 2015 Satoshi ITO, Yuichi SHIRAISHI, Kenichi CHIBA

1. General

GFK is a parallelized version of Genomon-fusion. Genomon-fusion is a pip eline software that performs alignment of FASTQ files of whole transcrip tome sequencing data and detects fusion gene candidates. For further inf ormation, see below:

User guide: doc/UserGuide.pdf

Genomon-fusion web site: http://genomon.hgc.jp/rna/

contact address: Satoshi ITO (sito@hgc.jp)

2. How to run 2.1 Prerequisite

Parallel computer and the following software can be installed.

• Message Passing Interface (MPI)
• perl
• blat (ver.35)
• Bowtie (ver.0.12.7)
• samtools (ver.0.1.20)
• fasta36 (ver.36.3.5c)
• SOAP denovo-Trans (ver.1.0.4)
• bedtools (ver.2.14.3)

Internet connection is also required if you use automatic download of datasets by Makefile.

2.2 Prepare blat

First, prepare blat and FaToTwoBit (blat utility). Then, copy them in to bin directory of this package.

2.3 Prepare Makefile.in

Sample Makefile.in for K-computer and Linux is located under etc/. So, copy appropriate sample to the top directory where this README is located, open with an editor, and set GFKDIR to the top directory.

2.4 Download tools and reference data

Type "make download". This will download archives of external tools and reference data.

2.5 Compile tools and GFK binaries

Type "make tool" to prepare external tools, and type "make src" to prepare GFK binaries under ./bin.

2.6 Prepare reference files

Type "make ref" to prepare reference files under ./bin.

If you are using K-computer, this step takes more than 14 hours, so it is recommended to run as a background job as follows:

$ make ref > make-ref.log 2>&1 &

2.7 Prepare for test

Change directory to test. Then, type "make", and an archive of executables and scripts for submi tting jobs will be created. Input data sequence1.txt and sequenc2.txt of CCLE_COLO_783_RNA_08 are to be located in ./test/Input/Input1 direc tory.

2.8 Submit jobs

Run GFKpre.sh

$ cd Input $ ../../bin/GFKpre.sh ../input.txt $ ../../bin/GFKpre.sh -f ../input.txt $ cd ..

Run GFKalign (Submit GFKalign.sh on K-computer)

$ mpirun -np 624 ../bin/GFKalign Output

or

$ pjsub GFKalign.sh (on K computer)

Run GFKpost.sh

$ cd Output $ ../../bin/GFKpost.sh ../Input/GFKPostProcess.txt $ cd ..

Run GFKdedup (Submit GFKdedup.sh on K-computer)

$ mpirun -np 1 ../bin/GFKdedup Output

or

$ pjsub GFKdedup.sh (on K computer)

Run GFKdetect (Submit GFKdetect.sh on K-computer)

$ mpirun -np 44 ../bin/GFKdetect Output

or

$ pjsub GFKdetect.sh (on K computer)

2.9 Result

fusion.0.txt is the final result. Reference output is fusion.0.ref.