SEQanswers - Bowtie poroblem when mapping against short sequences, no positions.

Hi All,

I want to use Bowtie to align reads to exons and junctions. I have created fasta files of the junctions and exons, indexed them and so on. When I run bowtie I end up with aligned reads without mapping information.

Code:

WICMT-SOLEXA_100421_61T4HAAXX:6:25:11235:11821#0/1;0        4        *        0        0        *        *        0        0        CGGGGCATAGGGGTACTTCTCAAGTGGGGAATGCCATATGAAGTGGAGCATACATGGGGGCACACAATTCCA@#######################################################################        XM:i:0

WICMT-SOLEXA_100421_61T4HAAXX:6:25:11235:13629#0/1;1        4        *        0        0        *        *        0        0        GTCCCGGCTCACTCAACCTCCACTTCCCAGGTTCAAGCGATTCTCCTGCCTCAGGCTCCCAAGTAGCTGGGAGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGFCGGFGGFGFGDGGGGGGGGFGGECFEEFFEDFCFEEEFDBC        XM:i:0

WICMT-SOLEXA_100421_61T4HAAXX:6:25:11235:17639#0/1;1        4        *        0        0        *        *        0        0        CCAGACCGTATTCCACCGCTTCAGGGGCGGAAAGGAAGCGATCGCGCTCGGTATCACGTTCAATCTGTTCTAGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGEGGGGDFGGGGFEFFGGDGFGFFGEFGFFFDFGEGGGG        XM:i:0

I know that spaces and pipes in the reference names can be a problem, so I don't have those in my names. The reference names are however quite long (chr1:196945439-196945639:+:ENSG00000081237 and similar). Names such as ENSG00000081237_1_196945439_196945639 makes no difference.

I'm using bowtie version 0.12.7.

Would truly appreciate some help!
Boel