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  • 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
    Last edited by Boel; 01-14-2011, 09:15 AM. Reason: typo

  • #2
    Problem solved.

    The flag is 4 = unmapped reads.

    Unable to delete my first message - sorry about that.

    Comment

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