I've been doing some test bacterial assy. running Canu ver 1.6 on some Sequel data. All works fine with extracted fastq or fasta data, but it fails if I try to pass the subreads.bam file- even though the program sees and begins the correction process before dying.
Should I be able to pass the subreads.bam or is this verboten? I have more detailed info. on script and errors to share, if this is an approach that one should be able to take.
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written
by
wlorenz •
1 answer
You can use a tool like bamtofastq to extract reads and pass these in. I'm not sure if BAM is an allowed input these days, but I don't think so.
bamtofastq filename=m54055_170517_074454.subreads.bam > 1K2_dig_subreads.fastq
You can find this in biobambam, available via bioconda.
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