Does anyone know of a script that allows one to convert Qual scores from a fastq file in order to map w/ BWA or Bowtie using the command line? I'm familar with the Galaxy tools function, but Galaxy has really been unreliable lately, I'd love to move away from it whenever possible.
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The qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format. The galaxy fastq groomer changes the qual score format to allow bwa or bowtie compatibility. I would like to run that script from the command line, and I wondered if anyone knew where to find it.
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Originally posted by Giles View PostThe qual portion of fastq comes in different varieties. Bwa and bowtie only accept one format...
Code:bowtie: --phred-33 (default) or --phred-64 bwa aln: (default is Phred+33, no option required) or -I (Phred+64).
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There are several other options for doing the conversion if you need to, e.g. EMBOSS seqret
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