which one indicate strand on bowtie outputs?

[tujchl]

HI everyone:
I use bowtie to map reads to genome on Galaxy using recommend option. and results like below (just one read show here):
HWUSI-EAS455_0034_FC630CNAAXX:4:1:1045:9169#0/1 16 chr10 10711690
255 40M * 0 0 GGATGTTGGAGTGCCCAGTGTACTCCATTTCAAAATACTA
HHHHHHDGHGHHHHGHHHHHHFGDGDGHHFHHHHHHHGGG XA:i:0 MD:Z:40 NM:i:0

could you point out which is indicate strand of my reads mapped to? I known 16 on the 2nd column indicates - and 4 is nomatch and do you know 0 indicates what? (0 is highly prevail in my data)

By the way there are always 0,4,16 in my data, Is it normal?

[ttnguyen]

You may want to refer to these for further information about SAM format:

http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output

http://samtools.sourceforge.net/SAM1.pdf

It is normal to output 0,4,16 often. You can use the code below to count the number of 0, 4, 16,.... in your SAM. In SE data, the proportion of reads mapped to forward strand (0) should be approximately equal to the proportion of reads mapped to reverse strand (16).

awk 'BEGIN {FS=OFS="\t"} {a[$2]++} END{for (i in a) print i, a[i]}' SAM_FILE

[volks]

this might be of interest to you: http://picard.sourceforge.net/explain-flags.html

[tujchl]

Got it! thank you