arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
140 stars 85 forks source link

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