CAGEscan mapping protocol: Difference between revisions
From Wiki
Jump to navigationJump to search
(Why the CAGEscan 3′ reads are trimmed.) |
(The 9 first bases of the CAGEscan 5′ reads are trimmed.) |
||
| Line 2: | Line 2: | ||
5' and 3' paired-end fastq files |
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 (<code>GGG</code>). |
|||
=== 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 [http://pubmed.gov/9973624 Mizuno et al., 1999] for example of priming over mismatches. |
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. |
||
Revision as of 18:42, 22 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 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
