@article{mmquant,
    author  = {Zytnicki, Matthias},
    title   = {mmquant: how to count multi-mapping reads?},
    journal = {BMC Bioinformatics},
    year    = {2017},
    volume  = {18},
    number  = {1},
    pages   = {411}
}

@article{subread,
    author  = {Liao, Yang and Smyth, Gordon K. and Shi, Wei},
    title   = {featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
    journal = {Bioinformatics},
    volume  = 30,
    number  = 7,
    pages   = {923--930},
    year    = 2014
}

@article{htseqcount,
    author  = {Anders, Simon and Pyl, Paul Theodor and Huber, Wolfgang},
    title   = {HTSeq—a Python framework to work with high-throughput sequencing data},
    journal = {Bioinformatics},
    volume  = 31,
    number  = 2,
    pages   = {166-169},
    year    = 2015
}

@Article{watson,
    author  = {Robert, Christelle and Watson, Mick},
    title   = {Errors in RNA-Seq quantification affect genes of relevance to human disease},
    journal = {Genome Biology},
    volume  = {16},
    number  = {1},
    pages   = {177},
    year    = {2015}
}

@article{samtools,
    author  = {Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup},
    title   = {The Sequence Alignment/Map format and SAMtools},
    journal = {Bioinformatics},
    volume  = {25},
    number  = {16},
    pages   = {2078--2079},
    year    = {2009}
}

@article{tophat2,
    author  = {Kim, Daehwan and Pertea, Geo and Trapnell, Cole and Pimentel, Harold and Kelley, Ryan and Salzberg, Steven L.},
    title   = {TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions},
    journal = {Genome Biology},
    year    = 2013,
    volume  = 14,
    number  = 4,
    pages   = {R36}
}

@article{star,
    author  = {Dobin, Alexander and Davis, Carrie A. and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R.},
    title   = {STAR: ultrafast universal RNA-seq aligner},
    journal = {Bioinformatics},
    volume  = 29,
    number  = 1,
    pages   = {15--21},
    year    = {2013}
}

@article{deseq2,
  author  = {Love, Michael I. and Huber, Wolfgang and Anders, Simon},
  journal = {Genome Biology},
  number  = 12,
  pages   = {550},
  title   = {{Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}},
  volume  = 15,
  year    = 2014
}

@article{data,
  author  = {Akula, N and Barb, J and Jiang, X and Wendland, J R and Choi, K H and Sen, S K and Hou, L and Chen, D T W and Laje, G and Johnson, K and Lipska, B K and Kleinman, J E and Corrada-Bravo, H and Detera-Wadleigh, S and Munson, P J and McMahon, F J},
  journal = {Molecular Psychiatry},
  pages   = {1179--1185},
  title   = {{RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder}},
  volume  = 19,
  year    = 2014
}

@article{entrez,
  author  = {Maglott, Donna and Ostell, Jim and Pruitt, Kim D and Tatusova, Tatiana},
  journal = {Nucleic Acids Research},
  pages   = {D54--D58},
  title   = {{Entrez Gene: gene-centered information at NCBI}},
  volume  = 33,
  year    = 2015
}

@article{ensembl,
  author  = {Zerbino, Daniel R and Achuthan, Premanand and Akanni, Wasiu and Amode, M Ridwan and Barrell, Daniel and Bhai, Jyothish and Billis, Konstantinos and Cummins, Carla and Gall, Astrid and Girón, Carlos García and Gil, Laurent and Gordon, Leo and Haggerty, Leanne and Haskell, Erin and Hourlier, Thibaut and Izuogu, Osagie G and Janacek, Sophie H and Juettemann, Thomas and To, Jimmy Kiang and Laird, Matthew R and Lavidas, Ilias and Liu, Zhicheng and Loveland, Jane E and Maurel, Thomas and McLaren, William and Moore, Benjamin and Mudge, Jonathan and Murphy, Daniel N and Newman, Victoria and Nuhn, Michael and Ogeh, Denye and Ong, Chuang Kee and Parker, Anne and Patricio, Mateus and Riat, Harpreet Singh and Schuilenburg, Helen and Sheppard, Dan and Sparrow, Helen and Taylor, Kieron and Thormann, Anja and Vullo, Alessandro and Walts, Brandon and Zadissa, Amonida and Frankish, Adam and Hunt, Sarah E and Kostadima, Myrto and Langridge, Nicholas and Martin, Fergal J and Muffato, Matthieu and Perry, Emily and Ruffier, Magali and Staines, Dan M and Trevanion, Stephen J and Aken, Bronwen L and Cunningham, Fiona and Yates, Andrew and Flicek, Paul},
  title   = {Ensembl 2018},
  journal = {Nucleic Acids Research},
  volume  = {46},
  number  = {D1},
  pages   = {D754--D761},
  year    = 2018
}