CAGEscan mapping protocol

Input

5' and 3' paired-end fastq files

5′

The 9 first bases of the 5′ reads are trimmed. The 6 first are the sequence index (“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