gian77/rcode-for-microbiome

Scripts for analyzing microbiome data

rcode-for-microbiome's Issues

Get SILVA reference files

We will need SILVA sequence alignment to align our sequences to rrnDB to match them to the right region within the gene.

We will need the recreates SEED database form [Mothur] (https://mothur.org/) form this link: https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v138_1.tgz

Generate a todo list for the project

One interesting thing you can do to keep your project organized is to use the Issue feature of Github to build a todo list of things you will need need for the project.

• 1. Download 16S operons

The rrnDB has downloads (https://rrndb.umms.med.umich.edu/) that we can use:

(https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.7_pantaxa_stats_RDP.tsv.zip
(https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.7_pantaxa_stats_NCBI.tsv.zip
(https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.7_16S_rRNA.fasta.zip
(https://rrndb.umms.med.umich.edu/static/download/rrnDB-5.7.tsv.zip)

These files will be downloaded in data/raw/

• 2. Download SILVA alignments

We will need SILVA sequence alignment to align our sequences to rrnDB to match them to the right region within the 16S gene.

• 3. Instal [Mothur] (https://mothur.org/) and dowload the SEED database form this link: https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v138_1.tgz