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<p><span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">Hi, </span></p>
<p><span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;"><br>
</span></p>
<p><span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;"> I am trying to use khmer to diginorm my illumina data and I have some questions about it: </span><br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
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<span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">1. I diginormed my data following the Eel Pond mRNAseq Protocol. The N50 of the assembly is 1242, smaller
than the assembly from the non-diginormed data, and also the number of the contigs is half of the non-diginormed. Is this normal that both assembly size and N50 becomes smaller?</span><br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">2. Because I got the data with adapter trimmed off, so I passed the step 1 and directly went to the
interleave step. Does this cause any problems in the downstream process?</span><br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;"> 3. After splitting the *.pe file into left.fq and right.fq, the left.fq has a size of 1.7gb, and thr
right.fq 1.4gb. Is this okay?</span><br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<br style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">
<span style="color: #282828; font-family: 'microsoft yahei ui', 'microsoft yahei', 微软雅黑, simsun, 宋体, sans-serif; font-size: 15px; background-color: #ffffff;">Thank you very much. I appreciate your time and patience.</span><br>
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<p>Shu Chen</p>
<p>Ph.D. Student</p>
<p>Department of Agronomy and Soils</p>
<p>RM 165, Funchess Hall </p>
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