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
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