Extend rat gene models with CAGEscan: Difference between revisions
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(The raw FASTQ CAGEscan reads must be trimmed.) |
(Index sequences for rat CAGEscan libraries.) |
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== Made from RNA 10009-101B8 == |
== Made from RNA 10009-101B8 == |
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10009-101B8 is the same RNA as used for CNhs10614, the ‘Universal RNA - Rat Normal Tissues’ |
10009-101B8 is the same RNA as used for CNhs10614, the ‘Universal RNA - Rat Normal Tissues’ HelicosCAGE library. |
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* NCig10012: 2 × 54 bp CAGEscan library, 6,903,269 reads. |
* NCig10012: 2 × 54 bp CAGEscan library, 6,903,269 reads. Index sequence <code>GCTCAG</code>. |
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* NCig10071: 2 × 36 bp experimental CAGEscan, 2,893,6176 reads, |
* NCig10071: 2 × 36 bp experimental CAGEscan, 2,893,6176 reads. Index sequences <code>ACAGATGCTATA</code>, <code>ATCGTGGCTATA</code>, <code>CACGATGCTATA</code>, <code>CACTGAGCTATA</code>, <code>CTGACGGCTATA</code>, <code>GAGTGAGCTATA</code>, <code>GTATACGCTATA</code>, <code>TCGAGCGCTATA</code>. |
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* NChi10001: 2 × 51 bp CAGEscan library (HiSeq test run), 9,662,576 reads. |
* NChi10001: 2 × 51 bp CAGEscan library (HiSeq test run), 9,662,576 reads. Index sequence <code>GCTCAG</code>. |
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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]] on what to trim from the reads before aligning. |
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Revision as of 17:29, 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.
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 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.
