I have a set of coordinate sorted, mapped BAM files for SARS-CoV-2 sequencing data through Nanopore MinION. that I need to generate paired fastq files for.
When I traditionally name sort the BAM files, run
samtools fixmate and then
bedtools bamtofastq, my paired fastq files are empty. When I run samtools flagstat on my bam files, I see that read1 and read 2 are 0:
52244 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 737 + 0 supplementary 0 + 0 duplicates 52244 + 0 mapped (100.00% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 0 + 0 properly paired (N/A : N/A) 0 + 0 with itself and mate mapped 0 + 0 singletons (N/A : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)
I am not fully familiar with Nanopore data so what is the best way to extract paired reads from my BAM files or are there any intermediate steps I am missing?