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Bamfilter outputting .fa instead of .fq #99
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I'm also running into this issue. |
It's not in the web documentation on the site (https://blobtools.readme.io/docs/bamfilter), but you can output fastq using the (blobtools) [user@server blobtools]$ blobtools bamfilter -h
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great thanks for your help! |
Hello,
Thanks for blobTools, it's a really wonderful piece of software. I'm using the bamfilter module to extract all sequences mapping to contigs of a particular taxon and though the original sequences were pe .fq files, bamfilter outputs .fa files. Do you know why this is and how to ensure .fq as the output format?
My bam file was produced using bwa mem and then gatk.
Cheers,
Theo
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