[khmer] filter-below-abund.py fastq scores from previous file

[Eric McDonald]

I believe that the 'filter-below-abund.py' script trims sequences. So, your
Perl script may need to also truncate the quality scores line down to the
length of the trimmed sequences.

By the way, we are working on getting the scripts to output FASTQ if they
receive FASTQ inputs, but that functionality is not ready yet. You're
definitely not the only person interested in that functionality. ;-)

Hope that helps,
  Eric



On Wed, Apr 10, 2013 at 8:13 AM, Jens-Konrad Preem <jpreem at ut.ee> wrote:

> Hi,
> I have just a quick question. Filter-below-abund takes a fastq file and
> outputs a fasta file.
> Can I make use of a Perl script that would take the names from the
> resulting file and add the quality scores from the previous file. As I
> understand nothing happens to the names or sequences - some of them just
> get culled.
>
> I want to try out the normalized data with some paired end reads
> assemblers that use quality scores/fastq files.
> I think its easier for me to write such Perl script than to modify
> filter-below-abund.py to output fastq.
>
> Not much of a python guy - though it seems that there shouldn't be too
> much work on replacing screed.fasta with screed.fastq etc., but I find it
> is quite often easier to write a few lines than to parse what someone else
> wrote and why and then try to modify it :D.
>
> Jens-Konrad Preem, MSc., University of Tartu
>
>
>
>
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-- 
Eric McDonald
HPC/Cloud Software Engineer
  for the Institute for Cyber-Enabled Research (iCER)
  and the Laboratory for Genomics, Evolution, and Development (GED)
Michigan State University
P: 517-355-8733
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