make.contigs output quality file

Commands in mothur
1

Hi,
When I use make.contigs, I see that a fasta file is generated.
Is there a way to obtain also a quality file from the generated contigs.
This will be useful to perform quality trimming post contig generation.
Thanks so much,
Carles.

1 Like
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Dear Carles, I have asked the same question in the forum recently. Despite the server problem, the corresponding thread is still there:
http://mothur.ltcmp.net/t/how-to-generate-qfile-for-joined-paired-ends-reads/2295/1
And the manual page for make.contigs says that (this is in the Google cache page): “1.35.0 - Improved speed, added quality score data, added kmer aligning method.” but I don’t really see how this can be done.
Yours,
Maxime

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Thanks Maxime.

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I am interested in a solution if you can find one (I will also search and post it in case I find something).
Maxime

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Re-,
Although this does not appear clearly on the wiki at the time I’m writing, Sarah Westcott confirmed to me that make.contigs() in the latest release of mothur (1.35) has the ability to output a quality file. For that you must input either fastq files or fasta and qfiles into the make.contigs command. The output is not fastq, rather it is a pandaseq-based quality score data. I don’t really get the details, but this quality file can’t be processed as regular fastq files.
Maxime

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Thanks, MaximeG - you are correct. We finally folded to y’all’s pressure and incorporated the quality score calculations from PandaSeq, but I’m still not sure what people plan on doing with them since they aren’t quite the same as the Phred quality scores.

Pat