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Question: Mapping Phred+64 encoded reads with Bowtie2
0
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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?

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1

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

ADD REPLYlink 9 months ago
genomax
68k
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0

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 9 months ago
Denis
• 70

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