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
QNAME: SRR322837.8.1
FLAG: 99
RNAME: chr1
POS: 163761156
MAPQ: 255
CIAGR: 36M
MRNM: =
MPOS: 163761301
ISIZE: 181
SEQ: NTGGATACTATTTTGCCATAAAAAAATGAATAAAAT
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
SEQ: TATTATGTCAATCTATGAAGAAGGACGGCGAGGTGA
QUAL: GDBE@B>EEGDB=BD-=GG>GGGEDDG<GBGD8GB?
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 Pairs?
Thanks,
Jianguang Du