extra data for our 454 paper (Genes, Genomes, Genetics 2012/13)

  1. Visualizing reads on teh UCSC genome browser

    • all consensus-split-mapped-molecules ("CSMMs" - meaning each intron in the mapping respects the splice site consensus including those of Tilgner et al, PNAS, 2014 and of Sharon et al, NBT 2013) can be inspected visually on the UCSC browser using this link

  2. well-mapped alignments for the K562 cell line

    • are here
    • note, that alignments overlapping ribosomal RNA genes have been removed
    • these alignments were used in figure 1e
    • note also, that this file contains a comment line for display on the UCSC browser. Uploading all reads to the UCSC browser at once may however take a lot of time. We would advise to rewrite the comment line and all alignments in a genomic region into a smaller file and to upload this smaller file to the UCSC browser
    • on a linux-terminal you could select all alignments located on chr11 between 10Mb and 11Mb using the following command (and then submit the result to the UCSC browser)
      1. zcat supplementalFileS1.gff.gz | awk '{if($1=="track"){print; next;} if($1!="chr11" || $5<10000000 || $4>11000000){next;} print ; }' > test.gff
      2. gzip test.gff

  3. well-mapped alignments for the HelaS3 cell line

    • are here
    • these alignments were used in figure S2e
    • otherwise, similar comments as to the K562 cell line apply