BigelowLab edna-dada2 issues

BigelowLab / edna-dada2

Maine eDNA dada2

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update R?

#37 btupper opened 9 months ago
0
issues creating phyloseq object in dada2 vis script

#36 sydneygreenlee opened 9 months ago
2
subset samples by # of reads step omitted from dada2 vis script

#35 sydneygreenlee closed 7 months ago
2
Add raw sequencing reads to charlie

#34 sydneygreenlee closed 7 months ago
1
incomplete preprocess run for PacBio 18S sequences

#33 abooker10 closed 9 months ago
4
Pacbio code block issue

#32 btupper closed 9 months ago
4
error that causes dada2 to terminate - my first time using the workflow so I may not have everything installed correctly

#31 abooker10 closed 1 year ago
3
Truncating reads to 1

#30 robinsleith closed 1 year ago
24
Citing the pipeline

#29 robinsleith opened 1 year ago
3
Dealing with "blank" samples

#28 robinsleith opened 1 year ago
12
assign_taxonomy outputs

#27 btupper closed 2 years ago
12
Strip unnecessary characters from sample names (e.g. fastq.gz)

#26 robinsleith closed 2 years ago
1
cutadapt problem

#25 robinsleith closed 2 years ago
4
sample.names number problem

#24 robinsleith closed 3 years ago
2
low priority: friendly error if no files in input_files

#23 robinsleith closed 3 years ago
2
edna_user_installer.R normalizePath error

#22 robinsleith closed 3 years ago
6
truncLen numeric

#21 robinsleith closed 3 years ago
16
Adding quantile_min to yaml

#20 robinsleith closed 3 years ago
2
throw human readable error if no reads make it past cutadapt

#19 robinsleith closed 3 years ago
23
Auto populate paths

#18 robinsleith closed 2 years ago
1
overlap default to yaml

#17 robinsleith closed 3 years ago
2
multistep ASV workflow

#16 btupper closed 2 years ago
3
harmonize input/output listings of filter_and_trim()

#15 btupper closed 3 years ago
1
Remove unnecessary files from output

#14 robinsleith opened 3 years ago
0
Add explanation of overlap output and EE output to wiki page, maybe cleanup column names for these?

#13 robinsleith opened 3 years ago
1
Script to update (install) dadautils so that all users can easily get updates as we push them

#12 robinsleith closed 3 years ago
1
Once we have "final" workflow run a profiler to look at speed and which steps are slowest

#11 robinsleith closed 3 years ago
6
Output overlap.csv somewhere in workflow

#10 robinsleith closed 3 years ago
12
Transition to using quality_profile_pairs instead of plot_qualityProfiles

#9 robinsleith closed 3 years ago
13
git push error

#8 robinsleith closed 3 years ago
2
Should I be afraid of .save and .save1?

#7 robinsleith closed 3 years ago
5
Where/when to print maxEE information (before filter_and_trim)

#6 robinsleith closed 3 years ago
3
Add reference database name to output of assign_taxonomy

#5 robinsleith opened 3 years ago
8
PacBio Workflow

#4 robinsleith closed 3 years ago
8
Redesign example script and example configuration layout

#3 btupper closed 3 years ago
5
Two assign_taxonomy calls in my version of dada.R

#2 robinsleith closed 3 years ago
1
managing R packages

#1 btupper closed 4 years ago
2