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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/