hi, I'm working with RNA-seq data. I reverse complemented sequences in a fastq file using fastx reverse complement function adding the -Q 33 option. Without this option I got this error: "fastx_reverse_complement: Invalid quality score value (char '.' ord 46 quality value -18) on line 8". Now when I align using bowtie (bowtie ../../../E_coli -S -q -p 7 --ff -1 1AR002_noribo_1.fq -2 1AR002_noribo_rv_2.fq >prueba_R1_R2/ff.sam) I get the following error :
Saw ASCII character -54 but expected 33-based Phred qual. terminate called after throwing an instance of 'int'
Anybody has an idea of what could I be making wrong? any suggestion will be appreciated.