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 

For the forward read
QNAME:   SRR322837.8.1
FLAG:    99
RNAME:   chr1
POS:     163761156
MAPQ:    255
CIAGR:   36M
MRNM:    =
MPOS:    163761301
ISIZE:   181
QUAL:    %(,,')(())@@@2235885<<22222@@@######
OPT:     XA:i:1 MD:Z:0A35      NM:i:1

For the reverse read
QNAME:   SRR322837.8.2
FLAG:    147
RNAME:   chr1
POS:     163761301
MAPQ:    255
CIAGR:   36M
MRNM:    =
MPOS:    163761156
ISIZE:   -181
OPT:     MD:Z:29A6      NM:i:1

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 


Jianguang Du
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