I got reads from PacBio sequencing. The reads are in BAM format. I converted them into FASTQ format.
I both used the
samtools fastq tools to do that.
The problem I have is that I got the " ! " score for all bases of the sequences with both tools, which means the bases are all wrong. What is not good because the phred score I got with FASTQC is really good (and reads obtained with the PacBio tech are usually always good)