Comparing mapped reads

[RNAddict]

I have used Tophat to map reads to a reference sequences. I would like to identify reads that mapped to multiple sequences. Does anyone know how this can be accomplished?

E.g. I would like to be able to say, read 1 mapped to reference sequences 1, 3, 23, and 67.

The above would be ideal... but if that is not possible then something like reference sequence 3 had reads 1, 19, 394, 39291, etc. map to it.

Any ideas? I feel like this is probably pretty doable I am just a rookie though.

[kopi-o]

Look at the NH:i flag at the end of the line. This indicates how many loci the read mapped to. The third column shows which reference sequence the alignment is to.

[swaraj]

TO GET CLASSIFICATION OF MAPPED READS
"samtools view sorted.bam | awk '{print $2}' | sort | uniq -c"
#THIS GIVES A RESULT
83839545 0
83824316 16
6755765 256
6850132 272

HERE 0, 16, 256, 272 ARE TOPHAT FLAGS TO UNDERSTAND THEIR MEANING GO TO:http://picard.sourceforge.net/explain-flags.html

GIVES THE COUNT OF NUMBER OF UNIQUE READS MAPPED

"samtools view t24hpf_sorted.bam | awk '{print $1}' | sort | uniq -c"