Re: [Samtools-help] [Fwd: Re: sam question]

[Heng Li <lh...@sa...>]

Hello Jim,

In SAM, we allow a read stored in multiple records. Say the sequence  
of a read "rd1" is "acgttgca". Its first 4bp mapped to chr1:100 and  
the last to chr2:200. We may save the alignment as:

rd1 chr1 100 4M4H acgt
.... (other alignments)
rd1 chr2 200 4H4M tgca

I intend to reuse MRNM and MPOS fields to indicate the position of the  
other part. We may also add additional fields to keep this. I have not  
thought it through. I think SAM (or a slightly modified version of  
SAM) can store alignments on a De Brujin graph.

It is interesting to know you have a better way to compressed the  
sequence data. How is it achieved?

Thanks,

Heng

On 18 Mar 2009, at 22:03, Knight, James wrote:

> Excellent. Thank you.
>
> The sticking point I've run into with every alignment format has  
> been the belief that all reads can be aligned contiguously, despite  
> split alignments caused by rearrangements, by mapping transcript  
> data to the genome, and other examples I can think of.
>
> And, the inclusion of split alignments then allows for the  
> description of full alignments of DeBrujin graph assembly alignments.
>
> I just heard about the SAM/BAM format at the Genome Informatics  
> Alliance conference, and checked my internal alignment data  
> structures, finding that I'm using about 0.3 bytes per base to store  
> what looks like the same information. Is there interest in  
> discussing this?
>
> Jim
>
> --------------------------
> Sent using BlackBerry
>
>
> From: Tim Fennell
> To: Knight, James {454_~Branford}
> Cc: Toby Bloom ; sam...@li...
> Sent: Wed Mar 18 17:21:53 2009
> Subject: Re: [Fwd: Re: sam question]
>
> That's a great question Jim.  I don't know if there's a way in the  
> current spec to store the alignments of reads that span breakpoints  
> of transversions.  I haven't personally thought about this but I'm  
> cc'ing the samtools-help mailing list where other people involved in  
> the SAM spec may have an answer.  If not we should think about how  
> to encode this in the next iteration of the spec.
>
> -t
>
> On Mar 18, 2009, at 4:53 PM, Knight, James wrote:
>
>> What would happen with an inversion where one half of the read is  
>> in the opposite direction from the other?
>>
>> Jim
>>
>> --------------------------
>> Sent using BlackBerry
>>
>>
>> From: Toby Bloom
>> To: Knight, James {454_~Branford}
>> Sent: Wed Mar 18 16:29:06 2009
>> Subject: [Fwd: Re: sam question]
>>
>> Hope this answers your question.
>>
>> -------- Original Message --------
>> Subject:
>> Re: sam question
>> Date:
>> Wed, 18 Mar 2009 16:25:51 -0400
>> From:
>> Tim Fennell <tfe...@br...>
>> To:
>> Toby Bloom <bl...@br...>
>> References:
>> <49C...@br...>
>>
>>
>> Right.  We'd represent that as a single entry in the sam file with  
>> the
>> whole read.  The CIGAR string which records the alignment has
>> operators for encoding such events.
>>
>> The three operators of interest are:
>> 	I = insertion (bases in the read that are not in the reference)
>> 	D = deletion (bases in the reference that are not in the read)
>> 	N = skip (like a deletion, but intended to be longer and imply a  
>> non-
>> deletion event like splicing)
>>
>> So if you had a 300 base read that had a small insertion after 30
>> bases and then hit a splice site at 150 bases and the next exon is
>> 10,000 bases away you might have a cigar string that looks like this:
>> 	30M4I150M10000N126M
>>
>> -t
>>
>>
>
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