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.
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
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'm using bowtie version 0.12.7.
Would truly appreciate some help!
Boel
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