title: TopHat-Recondition: a post-processor for TopHat unmapped reads.
abstract: BACKGROUND
  TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format - the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for aligned sequencing reads, thus correct format implementation is paramount for software interoperability and correct analysis. However, TopHat writes its unmapped reads in a way that is not compatible with other software that implements the SAM/BAM format.
  
  
  RESULTS
  We have developed TopHat-Recondition, a post-processor for TopHat unmapped reads that restores read information in the proper format. TopHat-Recondition thus enables downstream software to process the plethora of BAM files written by TopHat.
  
  
  CONCLUSIONS
  TopHat-Recondition can repair unmapped read files written by TopHat and is freely available under a 2-clause BSD license on GitHub: https://github.com/cbrueffer/tophat-recondition .
authors.affiliation: Division of Oncology and Pathology, Department of Clinical Sciences, Lund University Cancer Center, Lund University, Medicon Village Building 404-B2, Lund, 223 81, Sweden.
authors.forename: Christian
authors.initials: C
authors.lastname: Brueffer
authors.affiliation: Division of Oncology and Pathology, Department of Clinical Sciences, Lund University Cancer Center, Lund University, Medicon Village Building 404-B2, Lund, 223 81, Sweden. lao.saal@med.lu.se.
authors.forename: Lao H
authors.initials: LH
authors.lastname: Saal
mesh_terms: D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D012326:RNA Splicing; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D012313:RNA
keywords: Deep sequencing; RNA-seq; Sequence alignment; Sequence analysis