data for our SLR-RNA-Seq paper of human and mouse brain



  1. Visualizing reads on the UCSC genome browser

    • all consensus-split-mapped-molecules ("CSMMs" - meaning each intron in the mapping respects the splice site consensus) can be inspected visually on the UCSC browser using this link . Note that on this session, the reads from the current Nature Biotech paper (Tilgner et al., NBT 2015) are in a turquoise color. You will also find further datasets from three previous papers (Tilgner et al, GGG 2013, Sharon et al, NBT 2013, and Tilgner et al, PNAS 2014).



  2. consensus-split-mapped-molecules ("CSMMs" - meaning each intron in the mapping respects the splice site consensus) for human and mouse brain can be found

    • here for human brain ,
    • here for mouse brain 1
    • here for mouse brain 2
    • note, that alignments overlapping ribosomal RNA genes have been removed and that we only show spliced alignments
    • similarly treated data for
      • PacBio-data of the human HapMap cell-lines GM12878, GM12891 and GM12892 can be found here
      • PacBio-data of a panel of human organs can be found here
      • 454-data for the human cell lines K562 and HelaS3 can be found here. These reads are about half as long (ca. 520b but sequenced ten times as deeply as the PacBio data)



  3. ALL GMAP mappings in bam format


  4. Longread (SLR-RNA-Seq) fastq data

    • you will be able to download the raw inpt data from the SRA under http://www.ncbi.nlm.nih.gov/sra/?term=SRP049776 for human and http://www.ncbi.nlm.nih.gov/sra/?term=SRP050183 for mouse.
    • To make your life easier (no need to treat multiple separate files per sample at the SRA) you can also get all the assembled synthetic long reads (SLRs) in a combined fastq here



  5. Illumina 125-bp-PE fastq data (prior to assembly)

    • please get these directly from the SRA using
      • this link http://www.ncbi.nlm.nih.gov/sra/?term=SRP049776 for human
      • this link http://www.ncbi.nlm.nih.gov/sra/?term=SRP050183 for mouse