Utilising paired end data for use in MEGAN6
I have some paired-end shotgun data which I would like to analyze in MEGAN6. I've been told that MEGAN only accepts R1 data however as I already have the R2 was wondering if there was any way of utilizing it in my analysis.
I have been using Trimmomatic for my adapter trimming and was wondering if there would be an advantage in running it in PE mode and concatenating the paired and unpaired R1 reads rather than simply running it in SE mode on the R1 data, to begin with.
Is there any way I can use R2 data to improve the overall quality of my data or am I sticking only with R1? I'm only really interested in Taxonomic binning and functional analysis in this instance.
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andres.firrincieli
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A possible solution can be found here