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Forum: Bioinformatics 03-11-2010, 01:08 PM
Replies: 4
Views: 7,285
Posted By pieffe
Hi Nils, I think I was too quick to email...

Hi Nils,

I think I was too quick to email you a reply. I re-read your answer and you probably are right. The example in the SAM paper won't need N symbols in the read, since there are no...
Forum: Bioinformatics 03-11-2010, 12:40 PM
Replies: 4
Views: 7,285
Posted By pieffe
Thank you for your prompt reply. I think what you...

Thank you for your prompt reply. I think what you says makes sense. However, in the SAM specifications, there is an example where the alignment is spliced and the read does not have a 'N' symbol at...
Forum: Bioinformatics 03-11-2010, 09:22 AM
Replies: 4
Views: 7,285
Posted By pieffe
CIGAR strings and 'N' symbols

Just wondering if anybody can help me to understand the following example:


ref: AC GTACGT
r1 : ACCGTACGT
r2 : AC......T

Will the CIGARs be:

2M1I6M
Forum: Bioinformatics 06-01-2009, 08:09 AM
Replies: 0
Views: 1,231
Posted By pieffe
Question Help me understand MAQ indexing

Can anyone please help me clarify the following? Sorry if it is a dumb question!

I am reading the Methods' section of Maq paper.

If the first 28bp are indexed using the 6 templates, each read...
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