CAGEscan mapping protocol: Difference between revisions
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(CAGEscan paired-end read mapping protocol) |
(Why the CAGEscan 3′ reads are trimmed.) |
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5' and 3' paired-end fastq files |
5' and 3' paired-end fastq files |
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The 6 first bases of the 3′ reads are trimmed because they derive from to the random part (N6) of the reverse-transcription primer, and therefore may not reflect the RNA sequences accurately, since the reverse-transcriptase tolerates mismatches even on the last two bases. See [http://pubmed.gov/9973624 Mizuno et al., 1999] for example of priming over mismatches. |
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== Output == |
== Output == |
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Revision as of 14:14, 22 March 2011
Input
5' and 3' paired-end fastq files
The 6 first bases of the 3′ reads are trimmed because they derive from to the random part (N6) of the reverse-transcription primer, and therefore may not reflect the RNA sequences accurately, since the reverse-transcriptase tolerates mismatches even on the last two bases. See Mizuno et al., 1999 for example of priming over mismatches.
Output
Mapped paired-end tags in BAM format
