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limey-bean / Anacapa

Written by Emily Curd (eecurd@g.ucla.edu), Jesse Gomer (jessegomer@gmail.com), Gaurav Kandlikar (gkandlikar@ucla.edu), Zack Gold (zjgold@ucla.edu), Max Ogden (max@maxogden.com), Lenore Pipes (lpipes@berkeley.edu)and Baochen Shi (biosbc@gmail.com). Assistance was provided by Rachel Meyer (rsmeyer@ucla.edu).
MIT License
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Runnind using dada2 version 1.22 #64

Open Sbu211 opened 2 years ago

Sbu211 commented 2 years ago

Hi lime-bean

I am a Masters student at the University of Johannesburg, South Africa. My project entails using eDNA metabarcording as a tool to study estuarine meacroinvertebrates. Therefore the Anacapa toolkit is so essential for me to grasp and utilize for my project (by the way thank you for this toolkit)

I would like to inquire

I currently have dada 2 version 1.22 installed on my R(version 4.1.3) on my Linux ubuntu. The script (anacapa_QC) works well until the dada2 pipeline. I cant seem to get files in my out directory dada out folder. Checking the run log I see it halts the process and requires I install dada2 1.16.

Would it be possible to tweak the scripts to allow the use of dada2 version 1.22? If so how would I go about this? i.e do I change the anacapa_config.sh script or?

gauravsk commented 2 years ago

Hi Sibusiso - thanks for using the toolkit. I am not actively maintaining anacapa but here's my suggestion -

If there are not specific features in Dada2 v1.2.2 that are essential for your work, it might be easier to install an older version of dada2 than to change the anacapa configs. You can install dada2 v1.16 as follows in R:

install.packages("devtools")
library("devtools")
devtools::install_github("benjjneb/dada2", ref="v1.16") # change the ref argument to get other versions