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-   -   Bowtie not mapping (even) perfect matches ? (http://seqanswers.com/forums/showthread.php?t=27166)

yvan.wenger 02-05-2013 06:17 AM

Bowtie not mapping (even) perfect matches ?
 
Hello everybody,

I am a little worried since about half of my reads do not align, although they have exact full-length matches in the my dataset.

I run bowtie with the command line:

./bowtie-0.12.9/bowtie myindex -a -S -p 32 -r ibis100.raw ibis100.sam

As the command line says, I used raw reads without quality scores as an input.

Typical sam line for a read that matches 100% the reference:

10423427 4 * 0 0 * * 0 0 GTTATTCATTCACTACTACAGCTGAGCGTGAAATTGTAAGAGATATTAAAGAGAAACTTAGTTATGTAGCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XM:i:0

The vast majority of reads are perfect alignments when checked using blast, my understanding is that the -a option should cause them to be reported all, and still, they do not align properly.

Has anybody any thought about what could be the cause of that? I find it really weird and have not been able to find an explanation so far.

All the best,

Yvan


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