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
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:1MD:Z:0A35NM: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:29A6NM: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
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