Question: Keep quality score when correcting with Canu assembler?
0
gravatar for lizgzara
19 months ago by
lizgzara10
USA/San Bruno/San Francisco State University
lizgzara10 wrote:

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.

ADD COMMENTlink modified 19 months ago by Rohit1.3k • written 19 months ago by lizgzara10
0
gravatar for Rohit
19 months ago by
Rohit1.3k
European union
Rohit1.3k wrote:

There is a chance to create dummy fastq files with desired quality, check out this post

BioPython: convert fasta to fastq without quality score input file

You can also use pbh5tools for this purpose.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Rohit1.3k

Thank you! I ended up using Matt Shirley's code (from the link you provided) on the command line and it worked great!

ADD REPLYlink modified 18 months ago • written 18 months ago by lizgzara10
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