FusionCatcher Files

The files:
- reads_1.fq.gz
- reads_2.fq.gz

contain a small selection of short reads from:

[1]  SRR1548811 dataset (sample replicate 2, concentration log10 (pMol) = -8,57);
     SRA database http://www.ncbi.nlm.nih.gov/sra/?term=SRR1548811
     article: W.B. Tembe et al., Open-access synthetic spike-in mRNA-seq data
     for cancer gene fusions, BMC Genomics 2014, and

[2] RT-4 bladder cell line from Cancer Cell Line Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/dc45e1c0-e048-40b5-b48c-8caf3a7bc5ad

[3] EOL-1 acute myeloid leukemia cell line from Cancer Cell Line Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/f8df0beb-ac7f-450f-aa61-eef082f642ae

[4] U-118MG glioblastoma cell line from Cancer Cell Line Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/2c1a4f66-567b-46e0-9849-a869ac47ffc2

[5] Homo sapiens isolate case 2 IGH (D2-21)/MALT1 reciprocal breakpoint junction 
    genomic sequence, Accession GQ406059,
     http://www.ncbi.nlm.nih.gov/nuccore/GQ406059

[6] MUTZ-5 pre-B cell acute lymphoblastic leukemia cell line from Cancer 
    Cell Line Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/b82fb337-1b52-4146-b3a8-7878422a8027

[7] NALM-6 pre-B cell acute lymphoblastic leukemia cell line from Cancer 
    Cell Line Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/6fa77b04-bb16-49c5-8033-79dd76860c97

[8] SU-DHL-1 anaplastic large cell lymphoma cell line from Cancer Cell Line 
    Encyclopedia,
     https://portal.gdc.cancer.gov/legacy-archive/files/d6f97294-6cdd-4343-b40d-8277df996576

[9] Homo sapiens capicua-like protein/double homeodomain 4 fusion protein 
    (CIC/DUX4 fusion) mRNA, complete cds, Accession DQ388764,
     https://www.ncbi.nlm.nih.gov/nuccore/DQ388764.1

These short reads were selected manually such that they cover 17 already known fusion 
genes, which are:
- FGFR3-TACC3  (short reads from [2]),
- FIP1L1-PDGFRA  (short reads from [3]),
- GOPC-ROS1  (short reads from [4]),
- EWS-ATF1  (short reads from [1]),
- TMPRSS2-ETV1  (short reads from [1]),
- EWS-FLI1  (short reads from [1]),
- NTRK3-ETV6  (short reads from [1]),
- CD74-ROS1  (short reads from [1]),
- HOOK3-RET  (short reads from [1]),
- EML4-ALK  (short reads from [1]),
- AKAP9-BRAF  (short reads from [1]),
- BRD4-NUT  (short reads from [1]), 
- MALT1-IGH  (short reads from [5]),
- IGH-CRLF2  (short reads from [6]),
- DUX4-IGH  (short reads from [7]),
- NPM1-ALK  (short reads from [8]), and
- CIC-DUX4  (short reads from [9]).