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<div class="">(cc’ing the list back for the reply)</div>
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<div class="">Not sure re: whether khmer deals with this though it might explain the issue. You could run a count in your file for any empty lines, something like "zgrep -c '^$’ file_name.fastq.gz” (or pipe in the data via zcat if your system doesn’t have
zgrep). Not sure if cutadapt does anything silly like leave spaces, so you may need to adjust the grep accordingly. </div>
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<div class="">Both the sequence and the quality would be empty, so the # of records with empty lines should be count / 2.</div>
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<div class="">chris</div>
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<div class="">On Sep 16, 2015, at 9:08 PM, Will Shoemaker <<a href="mailto:wrshoema@umail.iu.edu" class="">wrshoema@umail.iu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hi Chris,
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<div class="">I checked the cutadapt docs and all the versions keep empty fastq reads and they don't have an option to remove them. I don't know how to check for empty fsatq reads using bash commands (I don't know what an empty fastq read looks like), but I
checked the number of reads in both the original and quality filtered fastq files and they have the same number of reads, so cutadapt is likely keeping empty reads. </div>
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<div class="">Is this still an issue for the newest version of khmer? </div>
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<div class="">Best,</div>
<div class="">Will</div>
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<div class="gmail_quote">On Wed, Sep 16, 2015 at 1:35 PM, Fields, Christopher J <span dir="ltr" class="">
<<a href="mailto:cjfields@illinois.edu" target="_blank" class="">cjfields@illinois.edu</a>></span> wrote:<br class="">
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<div style="word-wrap:break-word" class="">I may be mis-remembering this, but I recall cutadapt giving empty sequences with paired data before (maybe this has been fixed). Are any of the sequences empty?
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<div class="">chris</div>
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<div class="">On Sep 16, 2015, at 12:27 PM, Will Shoemaker <<a href="mailto:wrshoema@umail.iu.edu" target="_blank" class="">wrshoema@umail.iu.edu</a>> wrote:</div>
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<div dir="ltr" class="">Hello,
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<div class="">I am unable to merge pairs of MiSeq reads using the khmer scrip interleave-reads.py in khmer version 1.3. The R1 and R2 files have had the first 10 bases trimmed off and have been quality filtered using cutadapt v1.9. </div>
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<div class="">Using the command zcat file_name.fastq.gz | echo $((`wc -l`/4)) on each set of reads, I found that the number of reads in R1 and R2 is the same. </div>
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<div class="">The command I'm running is: </div>
<div class="">interleave-reads.py -o output.fastq.gz R1.fastq.gz R2.fastq.gz (file names changed for readability) </div>
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<div class="">My OS is Linux 2.6.32-573.3.1.el6.x86_64 x86_64</div>
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<div class="">Attached is a txt file of the khmer output.</div>
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<div class="">Could this be an issue of cutadapt changing the file format? I am able to run assemblies on cutadapt processed reads.<br clear="all" class="">
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<div class="">Best,</div>
<div class="">Will Shoemaker </div>
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<div dir="ltr" class="">Will Shoemaker
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<div dir="ltr" class=""><font face="arial, helvetica, sans-serif" color="#20124d" class="">Indiana University<br class="">
Graduate Student: Lennon Lab</font></div>
<div dir="ltr" class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class="">Evolution, Ecology, & Behavior Program</font></div>
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<div class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class="">Jordan Hall 238</font></div>
<div class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class=""><a href="mailto:wrshoema@umail.iu.edu" target="_blank" class="">wrshoema@umail.iu.edu</a><br class="">
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<div dir="ltr" class="">Will Shoemaker
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<div dir="ltr" class=""><font face="arial, helvetica, sans-serif" color="#20124d" class="">Indiana University<br class="">
Graduate Student: Lennon Lab</font></div>
<div dir="ltr" class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class="">Evolution, Ecology, & Behavior Program</font></div>
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<div class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class="">Jordan Hall 238</font></div>
<div class=""><font face="arial, helvetica, sans-serif" color="#20124d" style="font-size:small" class=""><a href="mailto:wrshoema@umail.iu.edu" target="_blank" class="">wrshoema@umail.iu.edu</a><br class="">
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