Mapping Phred+64 encoded reads with Bowtie2

Question

[Denis]

Hi, I faced with strange behavior of Bowtie2. I mapped reads with Phred+64 encoding by command:

bowtie2  --very-sensitive -x index -U R1.fastq -S Alignment.sam

I'm wondering why i didn't get any error message in that case? Is Bowtie2 able to determine reads encoding format automatically?

[GenoMax]

You should add --phred64 which indicates that qualities are Phred+64.

[Denis]

Thanks! But why i didn't get error by using this command line? I use this command a long time and only recently realized that the reads have Phred+64 encoding. How it may influence on the mapping results (everything looked well in resulted SAM file i usually got)?

[jean.elbers]

If I had to guess, the mapping results might be skewed as bowtie2 might (notice I said might) think that you have just really good higher quality sequences than you actually have. Not sure if bowtie2 can automatically determine the encoding of the reads or not.