I used bamToFastq to convert my bamfiles into R1 and R2 fastq files. I tried samtools fastq before but found it was erroneous (so many missing sequences). However, I still have an issue with bamTofastq from bedtools. When I add the read counts obtained from
grep -c "@" R1.fastq and
grep -c "@" R2.fastq, it is always slightly less than the count from the bamfile
samtools view -c in.bamfile. Why might this be the case? I haven't found any documentation to suggest that this is a normal thing. The R1 and R2 fastq counts should equal the counts in the bamfile so what am I doing wrong with the conversion??