Reads doubled when using `bamtofastq`

arq5x / bedtools

A powerful toolset for genome arithmetic.

http://code.google.com/p/bedtools/

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Reads doubled when using `bamtofastq` #167

Open jonathan-bravo opened 1 year ago

jonathan-bravo commented 1 year ago

Hello,

I am working with nanopore data, and after we do a host removal step we convert the resulting bam file to a fastq file for further processing. When using bedtools bamtofastq -i <BAM> -fq <OUT.fastq> I noticed that the reads are exactly doubled.

Cheers, Johnny