Tophat


Taking 4 (2x2) SE Illumina Runs and aligning to Abyss Assembly from Module 3.



TopHat Output


The tophat script produces a number of files in the directory in which it was invoked. Most of these files are internal, intermediate files that are generated for use within the pipeline. The output files you will likely want to look at are:

  1. accepted_hits.bam. A list of read alignments in SAM format. SAM is a compact short read alignment format that is increasingly being adopted. The formal specification is here.
  2. junctions.bed. A UCSC BED track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
  3. insertions.bed and deletions.bed. UCSC BED tracks of insertions and deletions reported by TopHat. 
    Insertions.bed - chromLeft refers to the last genomic base before the insertion. 
    Deletions.bed - chromLeft refers to the first genomic base of the deletion.