R expert Help run a bioinformatic pipline
Budget: $30 – $80 USD
DELIVERABLES
trimming barcodes and primers
bioinformatic pipeline script, possibly in DADA2 R (in case of some other open source software)
database with taxonomy
database with OTU/ASvs output
ADDITIONAL INFORMATION
Metabarcoding -targeting the bacterial community in seeds
I have extracted DNA from the seeds of a mountain plant, did PCR, and sequenced for targeting Bacteria 16S v4 region. I have 270 samples (plants individuals from which I have sampled seeds). Now I have raw sequences that need to be trimmed for barcodes and primers and run through a bioinformatic pipeline to obtain a classification database (Phylum to Genus/Species) that I will be able to use in R for further analysis. I preferentially use R but I am open to new open-source software for trimming and bioinformatics pipelines.
I have raw sequnnced fastaQ file or trimmed fastaq files (but those last one i could not run them trough DADA2)
for the pipline I am following https://benjjneb.github.io/dada2/tutorial.html
https://drive.google.com/drive/folders/1z5O8ExtvDqOYjp9L7Kn_w0sJ05HyfEwn?usp=sharing
here the link to the folder. There is a word file were I have tried to explain the work. Please ask me anything (i will tell you what i know). The two excel file are the excemple of output I am looking for. Then there are the data. The raw data and trimmed data.
thanks.
trimming barcodes and primers
bioinformatic pipeline script, possibly in DADA2 R (in case of some other open source software)
database with taxonomy
database with OTU/ASvs output
ADDITIONAL INFORMATION
Metabarcoding -targeting the bacterial community in seeds
I have extracted DNA from the seeds of a mountain plant, did PCR, and sequenced for targeting Bacteria 16S v4 region. I have 270 samples (plants individuals from which I have sampled seeds). Now I have raw sequences that need to be trimmed for barcodes and primers and run through a bioinformatic pipeline to obtain a classification database (Phylum to Genus/Species) that I will be able to use in R for further analysis. I preferentially use R but I am open to new open-source software for trimming and bioinformatics pipelines.
I have raw sequnnced fastaQ file or trimmed fastaq files (but those last one i could not run them trough DADA2)
for the pipline I am following https://benjjneb.github.io/dada2/tutorial.html
https://drive.google.com/drive/folders/1z5O8ExtvDqOYjp9L7Kn_w0sJ05HyfEwn?usp=sharing
here the link to the folder. There is a word file were I have tried to explain the work. Please ask me anything (i will tell you what i know). The two excel file are the excemple of output I am looking for. Then there are the data. The raw data and trimmed data.
thanks.