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 insertions in reference.
I guess that, if I am not misunderstanding, whenever a read has a I symbol in the cigar, other reads will either have P symbols in the cigar or they will have a N symbol in the read and a I symbol in the cigar.
Thanks again,
PF
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Originally posted by pieffe View PostThank 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 all, and yet the cigar has 32N in it.
I tried to use samtools to dig into this, but got even more confused. I guess I am going to ask to the authors of samtools for clarifications. I will post what I find out.
Thanks again!Last edited by nilshomer; 03-11-2010, 12:53 PM.
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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 all, and yet the cigar has 32N in it.
I tried to use samtools to dig into this, but got even more confused. I guess I am going to ask to the authors of samtools for clarifications. I will post what I find out.
Thanks again!
Leave a comment:
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Originally posted by pieffe View PostJust wondering if anybody can help me to understand the following example:
ref: AC GTACGT
r1 : ACCGTACGT
r2 : AC......T
Will the CIGARs be:
2M1I6M
2M6N1M
OR will it be:
2M1I6M
2M5N1M
In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?
Also, how do mappers determine segments with skipped N positions?
Thanks!Code:ref: AC GTACGT r1 : ACCGTACGT r2 : AC......T
You may want to send an email to the samtools-help mailing list for clarification.
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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
2M6N1M
OR will it be:
2M1I6M
2M5N1M
In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?
Also, how do mappers determine segments with skipped N positions?
Thanks!Tags: None
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