Question: Mapping Phred+64 encoded reads with Bowtie2
gravatar for Denis
5 months ago by
Denis140 wrote:

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?

ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 5 months ago by Denis140

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

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax74k

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)?

ADD REPLYlink modified 5 months ago • written 5 months ago by Denis140

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by jean.elbers1.3k
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