Mapping of tag sequences to the reference genome in Tassel 5 GBS v2 Pipeline

Question

[Denis]

I have a question regarding appropriate bowtie2 settings for mapping of tag sequences to the reference genome in Tassel 5 GBS v2 Pipeline. According to the Tassel 5 GBS v2 Pipeline manual (enter link description here) i should run bowtie2 with the following settings:

bowtie2 -p 15 --very-sensitive -x ../AGPv3/ZMAGP3_9103 -U tagsForAlign.fq -S tagsForAlignFullvs.sam

However, i found that tag sequences in FASTQ file have old Phred +64 quality encoding. In particular, all the bases in the FASTQ file have the same f letter in the quality string (the 4-th line). My question is : Should i add --phred64 option to the my bowtie2 command? So the correct command should look like:

bowtie2 -p 15 --phred64 --very-sensitive -x ../AGPv3/ZMAGP3_9103 -U tagsForAlign.fq -S tagsForAlignFullvs.sam