Howdy Jianguang,

There's a more complete description of the SAM format in "The Sequence
Alignment/Map format and SAMtools", Li et al, Bioinformatics (2009).  And
you can find the latest specification for the format at
samtools.sourceforge.net .

In the spec, the terminology for the ISIZE field has been changed to TLEN,
template length, to allow for sequencing technologies that produce more
than two sequenced segments.  The description there is "the number of
bases from the leftmost mapped base to the rightmost mapped base".

So I think to convert to "inner distance between mate pairs" you would
typically take ISIZE and subtract the lengths of the mates.  Note that for
some technologies that value could be negative (which just means the mates
overlap).  You might need to take into account whether the mates have been
mapped with proper orientation-- for example, if an inversion has flipped
one mate it has also carried that mate closer to or farther from the
other.

Bob H


> Hello Jianguang,
>
> On the Bowtie tool form itself, please find this text:
>
> Outputs
>
> The output is in SAM format, and has the following columns:
>
>    Column  Description
> --------  --------------------------------------------------------
>   1 QNAME  Query (pair) NAME
>   2 FLAG   bitwise FLAG
>   3 RNAME  Reference sequence NAME
>   4 POS    1-based leftmost POSition/coordinate of clipped sequence
>   5 MAPQ   MAPping Quality (Phred-scaled)
>   6 CIGAR  extended CIGAR string
>   7 MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
>   8 MPOS   1-based Mate POSition
>   9 ISIZE  Inferred insert SIZE
> 10 SEQ    query SEQuence on the same strand as the reference
> 11 QUAL   query QUALity (ASCII-33 gives the Phred base quality)
> 12 OPT    variable OPTional fields in the format TAG:VTYPE:VALUE
>
>
> The value of ISIZE is the total insert size for this read pair.
>
>
> Hopefully this helps!
>
> Jen
> Galaxy team
>
> On 8/16/12 2:34 PM, Du, Jianguang wrote:
>> Dear All,
>>
>> In order to figure out the Mean Inner Distance between Mate Pairs of my
>> paired-end RNA-seq datasets, I ran Bowtie (Map with Bowtie for Illumina)
>> with both forward and reverse datasets and mouse mm9 as reference
>> genome. Below I list the Bowtie output for only one pair of reads (I put
>> the fields on the left side):
>>
>> For the forward read
>>  ...snip...
>> Is the ISIZE the insert size? The difference between POS and MPOS is
>> 145bp, which is 36bp shorter than ISIZE (181). My question is: if
>> ISIZE does mean insert size, how should I convert INSIZE into Mean Inner
>> Distance between Mate Pairs?
>>
>> Thanks,
>>
>> Jianguang Du

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