Revision as of 17:33, 23 March 2011

Background

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

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′.

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

@@ Line 18: / Line 18: @@
 * NChi10001: 2 × 51 bp CAGEscan library (HiSeq test run), 9,662,576 reads. Index sequence <code>GCTCAG</code>.
-Bzipped FASTQ files are available in <https://fantom5-collaboration.gsc.riken.jp/webdav/home/plessy/FASTQ/>. See [[CAGEscan]] on what to trim from the reads before aligning.
+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: <code>name_lane_direction.fq.bz2</code>. The sequencer [[Dataset_introduction#Keywords.2C_jargon|lane]] is indicated but should not have importance. Direction 1 is 5′ and direction 2 is 3′.