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
___________________________________________________________ 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:
-- Jennifer Jackson http://galaxyproject.org