CAGEscan mapping protocol: Difference between revisions
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(The 9 first bases of the CAGEscan 5′ reads are trimmed.) |
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=== 5′ === |
=== 5′ === |
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The 9 first bases of the 5′ reads are trimmed. The 6 first are the |
The 9 first bases of the 5′ reads are trimmed. The 6 first are the ''index sequence'' (“barcode”) and the 3 next are the linker (<code>GGG</code>). |
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=== 3′ === |
=== 3′ === |
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Revision as of 17:33, 23 March 2011
Input
5' and 3' paired-end fastq files
5′
The 9 first bases of the 5′ reads are trimmed. The 6 first are the index sequence (“barcode”) and the 3 next are the linker (GGG).
3′
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
