Background

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

Data

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.

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′.

FASTQ sequences of sorted and trimmed reads can be retreived from the paired-end aligned BAM files (see below), that include unmapped reads.

To retrieve properly paired 5′ ends: samtools view -b -f 0x0042 [input] > [output]

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, ontological enrichment of shifted genes compared to the correctly annotated ones?
How many new genes with support(x)?
Investigate high confidence TSSs (evidence from both CAGE-methods)
Alternative promoters
Other

Alternative promoter
Definition to belong to a known promoter: Max shift allowed? The second cagescan tag falls in the known gene?
Filter: Seen with both Cagescan and hCage