Extend rat gene models with CAGEscan

Background

• Some rat gene models miss the real 5′ ends.
• HelicosCAGE and CAGEscan libraries are available from a “universal” rat RNA preparation.

Data

Made from RNA 10009-101B8

10009-101B8 is the same RNA as used for CNhs10614, the ‘Universal RNA - Rat Normal Tissues’ HelicosCAGE library.

• NCig10012: 2 × 54 bp CAGEscan library, 6,903,269 reads. Index sequence GCTCAG.
• NCig10071: 2 × 36 bp experimental CAGEscan, 2,893,6176 reads. Index sequences ACAGATGCTATA, ATCGTGGCTATA, CACGATGCTATA, CACTGAGCTATA, CTGACGGCTATA, GAGTGAGCTATA, GTATACGCTATA, TCGAGCGCTATA.
• NChi10001: 2 × 51 bp CAGEscan library (HiSeq test run), 9,662,576 reads. Index sequence GCTCAG.

Bzipped FASTQ files are available in <https://fantom5-collaboration.gsc.riken.jp/webdav/home/plessy/FASTQ/>. See CAGEscan_mapping_protocol on what to trim from the reads before aligning.

Name scheme: name_lane_direction.fq.bz2. The sequencer lane is indicated but should not have importance. Direction 1 is 5′ and direction 2 is 3′.

Goal

Contribute experimental evidence that extends and update the gene models in rat.

Key questions:

• How many rat “refseq” TSS’es are correct?
• How many rat “refseq” TSS’es are shifted, either 5’ or 3’?
• Function of shifted genes, are the shifted genes enriched for some function compared to the correct annotated ones?
• How many new genes with support(x)?
• Investigate high confidence TSSs(evidence from both CAGE-methods)
• Alternative promoters
• Other