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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" class="">wrshoema@umail.iu.edu</a>> wrote:</div>
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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 class=""><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_shoemakah&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=2hmDL9wRzmlU_2g0L0tNoUVmhlNMH4HLOevw22IEZds&s=83OIHhrZUaG5B6v_qoLzlJTxaI8_4EB_ZY-KTuz_aeg&e=" target="_blank" class="">@shoemakah</a><br class="">
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