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Hi,
I'm doing an alignment using Bowtie2 and want to know if is to reduce the values of phred. I need to do this to compare my results with a paid software I'm using, the CLC, which allows me to use a value equal to 20 phred. The bowtie2 by default has the value of phred equal to 33, which was what I used, since it is this type of file quality than my own sequencing.
I'm doing an alignment using Bowtie2 and want to know if is to reduce the values of phred. I need to do this to compare my results with a paid software I'm using, the CLC, which allows me to use a value equal to 20 phred. The bowtie2 by default has the value of phred equal to 33, which was what I used, since it is this type of file quality than my own sequencing.