Hi,
I’ve done a get.relabund on my shared file (stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.shared) to get relative abundance of each OTU in my samples. After this, I have identified manually the major OTUs of my relabund file with my tax file. In order to save a lot of time, is there a command to identify OTUs of my relabund file ?
Best regards,
Julien
I’m not really sure what you’re asking, but you can definitely parse the relabund file in R
I wasn’t very clear…
For example, for my sample A my relabund files look like :
OTU1 0,32456
OTU2 0,03498
OTU3 0,59873
OTU4 0,00123
…
With my tax file, I identidy my OTU one by one by hand. Not knowing anything on R, I make charts with Excel with my 10 most numerous OTUs. I was wondering if there is a way to make a relabund file with the name of my OTUs instead of identifying them one by one ?
By the way I’m open to any recommandation concerning R. Thanks a lot !
To complete my question…
My relabund file looks like
OTU1 0,8988
OTU2 0,0211
OTU3 0,1231
What it the command to switch from OTU numbers to OTU names ? For example :
Enterobacter 0,8988
Bacillus 0,0211
Klebsiella 0,1231
Thanks!
Hi, I am not sure I perfectly understand what you want to do but you might also try to use classify.otu with the parameter basis=sequence which will output the number of reads correspond to the different taxonomic levels in each sample. Hope this helps! Maxime
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Thank you so much… That’s exactly what I needed!