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Old 04-20-2016, 06:35 PM   #1
lguzmanz
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Location: Pacifica, CA

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Default Keep quality score when correcting with Canu assembler?

I am using Canu assembler to do a de novo assembly of PacBio data. I noticed that when I corrected my reads it produced a .fasta not a .fastq file, therefore loosing the quality score data of my original raw PacBio reads. Is there any parameter or option I can add so that the quality score is not lost when issuing the "canu -correct" command? Thank you!

P.S. I am trying to pipe the corrected reads to MIRA and MIRA requires quality scores when I run it on Geneious.
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Old 04-21-2016, 08:57 AM   #2
rhall
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The quality score would have to reflect the base quality of the corrected read. The easiest thing to do is estimate the base QV based on coverage in the correction (I would guess ~QV20), then fake the QV values in the fastq (same for every base).
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