<div dir="ltr">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.<div><br></div><div style>
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. ;-)</div>
<div style><br></div><div style>Hope that helps,</div><div style> Eric</div><div style><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 10, 2013 at 8:13 AM, Jens-Konrad Preem <span dir="ltr"><<a href="mailto:jpreem@ut.ee" target="_blank">jpreem@ut.ee</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
I have just a quick question. Filter-below-abund takes a fastq file and outputs a fasta file.<br>
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.<br>
<br>
I want to try out the normalized data with some paired end reads assemblers that use quality scores/fastq files.<br>
I think its easier for me to write such Perl script than to modify filter-below-abund.py to output fastq.<br>
<br>
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.<br>
<br>
Jens-Konrad Preem, MSc., University of Tartu<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><div>Eric McDonald</div><div>HPC/Cloud Software Engineer</div><div> for the Institute for Cyber-Enabled Research (iCER)</div><div> and the Laboratory for Genomics, Evolution, and Development (GED)</div>
<div>Michigan State University</div><div>P: 517-355-8733</div></div>
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