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Old 02-05-2013, 05:17 AM   #1
yvan.wenger
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Location: Switzerland

Join Date: Aug 2009
Posts: 30
Default 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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