Sample Junction BED files

Junction.bed and exon.bed files produced from RNA-seq alignment of Illumina sequence reads for four biological samples are provided below using TopHat with known and novel discovery allowed (version 1.2.0). These samples correspond to:

  1. Human embryonic stem cells
  2. Derived neural precursors

These files are available in a zip compressed archive here.


Sample data was obtained from NCBI's now discontinued Sequence Read Archive ( for the entries SRS011896, SRS011898, SRS011900 and SRS011902. Note: SRA is in the process of being discontinued, hence, FASTQ files may be unavailable.

For each of these samples, multiple sequence read files were downloaded and concatenated in FASTQ format. TopHat was run allowing for novel junction discovery and default settings as described here. Junction results were obtained directly from TopHat, while exon read counts were obtained using BEDTools as described here. An overview of how to build AltAnalyze RNA-seq input files can be found here.

To load in AltAnalyze, download version 2.0, extract and start the software, select the species database for "Homo sapiens" and proceed to "Process Junction Files".