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Old 04-24-2017, 09:50 AM   #1
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Location: Lubbock,TX.

Join Date: Apr 2017
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Default How to separate eukaryotic sequence reads from my metagenome data?


I have Illumina Hiseq data from leafhopper Empoasca fabae. It has two symbionts, Sulcia muelleri, and Nasuia deltocephalinicola. In my project, we sequenced head and bacteriome regions of 4 different leafhopper specimens. We want to know if they are any differences in bacterial populations between these specimens and also want to see if they are any new bacteria present in the head samples of leafhopper. As the genome of the leafhopper is not sequenced yet, I cannot map the reads to a reference genome and filter out the eukaryotic reads so that I can analyze the bacterial population. How can I solve this problem? Thank you very much.

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