SchlossLab Schloss_rrnAnalysis_mSphere_2021 issues

SchlossLab / Schloss_rrnAnalysis_mSphere_2021

Code Club project analyzing utility of ASVs

MIT License

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Trade off analysis of E/ASV threshold impact on lumping and splitting taxa

#37 pschloss closed 3 years ago
1
Quantify uniqueness of E/ASVs within and between species

#36 pschloss closed 4 years ago
0
Determine threshold needed to get 1 ASV per genome

#35 pschloss closed 4 years ago
0
Create ASVs

#34 pschloss closed 4 years ago
0
Refactor project to indicate that we're working with ESVs

#33 pschloss closed 4 years ago
0
Get a sense of the dominance and commonness of ASVs within a species

#32 pschloss closed 4 years ago
0
Measure specificity of ASVs for each taxonomic rank and region of 16S rRNA gene

#31 pschloss closed 4 years ago
2
How many ASVs describe a species and does that number plateau with the number of genomes?

#30 pschloss closed 4 years ago
1
Add annotation layer to plot to indicate average of averages

#29 pschloss closed 4 years ago
1
Determine the number of rrn operons across taxonomic ranks

#28 pschloss closed 4 years ago
0
Create report showing taxonomic distribution within rrnDB

#27 pschloss closed 4 years ago
0
Use the tax_id for each genome sequence to trace back the NCBI taxonomy

#26 pschloss closed 4 years ago
0
Separate RDP sequence classification into different columns for each genome

#25 pschloss closed 4 years ago
1
Create a mapping file to translate between genome id and taxonomic information

#24 pschloss closed 4 years ago
0
Compare genome-level ASVs across variable regions

#23 pschloss closed 4 years ago
0
Convert my R script from 2020-09-09 to a R markdown document

#22 pschloss closed 4 years ago
0
Update my README.md file to reflect what I'm using on my computer

#21 pschloss closed 4 years ago
0
Profile and optimize conversation of count_table to cont_tibble file

#20 pschloss closed 4 years ago
0
Convert wide count_table data frame to a tidy count_tibble data frame

#19 pschloss closed 4 years ago
0
For the V4 region, leading periods were not replaced

#18 pschloss closed 4 years ago
0
Create a table indicating number of times each unique sequence appears across genomes

#17 pschloss closed 4 years ago
0
Covert leading (and lagging) periods in alignments into hyphens to represent gaps

#16 pschloss closed 4 years ago
0
Replace spaces with underscores in fasta headers prior to initial alignment

#15 pschloss closed 4 years ago
0
Create rule to install mothur and update other rules to use mothur as prerequisite

#14 pschloss closed 4 years ago
0
Only touch files extracted from rrnDB archives if unzip is successful

#13 pschloss closed 4 years ago
0
Extract subregions from the 16S rRNA gene sequence data

#12 pschloss closed 4 years ago
0
Refactor code/get_rrndb_files.sh to parse path and filename

#11 pschloss closed 4 years ago
0
Create Makefile

#10 pschloss closed 4 years ago
0
Write script to automate installing mothur

#9 pschloss closed 4 years ago
1
Covert instructions from README files into bash scripts

#8 pschloss closed 4 years ago
1
Format README files to make use of markdown formatting

#7 pschloss closed 4 years ago
2
Download reference files using command line tools

#6 pschloss closed 4 years ago
1
Generate resource list related to ASVs

#5 pschloss opened 4 years ago
3
Align the rrnDB fasta file to SILVA SEED reference

#4 pschloss closed 4 years ago
1
Install mothur

#3 pschloss closed 4 years ago
1
Get SILVA reference files

#2 pschloss closed 4 years ago
0
Get files from rrnDB

#1 pschloss closed 4 years ago
1