benjjneb decontam issues

benjjneb / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

https://benjjneb.github.io/decontam/

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issues

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Interpreting results with low sample size / Alternatives?

#154 Skirnir3141 opened 1 week ago
2
Inconsistent Contaminant Detection in Decontam with Read Count Threshold

#153 blesso13 opened 2 weeks ago
1
prevalence method in Decontam not Identifying contaminants with a single control sample

#152 JayalalKJ opened 3 weeks ago
1
How to apply decontam to functional data

#151 Ivy-ops opened 1 month ago
3
Batch-specific contaminant detection or not?

#150 zztin opened 3 months ago
0
Importing dada2 output

#149 nadeaujay opened 4 months ago
3
Use of frequency-based decontam method on Meta-transcriptomics data

#148 achald7867 opened 4 months ago
1
decontam use

#147 Zarzarn95 opened 5 months ago
3
EPI2ME decontam Oxford nanopore sequencing

#146 CamillePhilippeSCI opened 7 months ago
2
Install issues

#145 acrowell09 opened 7 months ago
6
Can i use "frequency" without DNA concentration?

#144 kx11jkjk closed 8 months ago
3
Decontam error

#143 OluchiAroh closed 7 months ago
4
DNA concentrations for half of the samples are 0.1ng/ul before PCR. Can I do decontam?

#142 sihanbu opened 9 months ago
2
Removal of contamination based on a negative control occurs when all of "P = NA"

#141 1023011930 opened 10 months ago
16
Result vary as per sample size

#140 achald7867 opened 1 year ago
6
Selection of methods for different sample types and non-subjective strategy to select method and threshold

#139 cBundg opened 1 year ago
2
Prevalence mode pruning

#138 skose82 closed 1 year ago
2
a

#137 cafferychen777 opened 1 year ago
0
Problems with the decontamination of metagenomic data or viral data

#136 1023011930 opened 1 year ago
6
Best way to use controls for multiple batches?

#135 DrLCode opened 1 year ago
1
Is one negative control useless for this application?

#134 lowrda opened 1 year ago
2
Here more NAs exist inside the calculated P-value and are classified as FALSE (non-contaminated features).

#133 YMSen opened 1 year ago
3
How to use controls in multiple small batches over one experiment

#132 AlexaBennett opened 1 year ago
2
very cross-contaminated samples

#131 lauraDRH opened 1 year ago
6
isContaminant with batch option

#130 Martinique-F opened 1 year ago
2
extraction control, pcr control and "buffer" control

#129 doloacu closed 3 weeks ago
1
Probable bug in "getFromPS(ps, conc) : ng.DNA is not a valid sample-variable in the provided phyloseq object."

#128 roey-angel closed 1 year ago
2
is "quant_reading" DNA concentration in some units or total DNA

#127 Rob-murphys opened 1 year ago
5
Negative control count best practices

#126 Rob-murphys closed 1 year ago
3
Strange prevalence plot contamination in controls

#125 ladywaspzhu opened 1 year ago
1
Update tcontam

#124 hczdavid opened 1 year ago
0
Positive control contamination

#123 FarzanehRah opened 1 year ago
1
p.freq differs when using method="frequency" and method="auto/combined/minimum/either/both"

#122 zz77zz opened 1 year ago
1
Very few contaminant detected regarding to the total number of ASVs

#121 Mcouedel opened 1 year ago
1
When are assumptions for decontam violated?

#120 pslai opened 2 years ago
1
Export data from prevalent option

#119 K-Gutierrez closed 2 years ago
2
Problems with "prune_taxa"

#118 Englittrigfisk opened 2 years ago
1
"Biological ASVs" identified as contaminants / "Contaminant ASVs" not identified as contaminants

#117 tellafiela opened 2 years ago
2
DNA concentration inputs

#116 devinjones18 opened 2 years ago
1
Importing the data

#115 lynneitelson opened 2 years ago
7
Error in data.frame and Removed 3 samples with zero total counts (or frequency)

#114 Paty-Azevedo opened 2 years ago
4
Controls Removal prior to filtering contaminants using 'frequency'

#113 andrebolerbarros closed 2 years ago
3
Used rarefided or unrarefided feature-table

#112 suiweikang opened 2 years ago
3
What is false contaminant?

#111 dikiprawisuda closed 2 years ago
1
Distribution of score statistics varies based on exclusion/inclusion of batch parameter

#110 starcutie closed 2 years ago
0
A LOT of contamination in controls

#109 sash2566 opened 2 years ago
1
prevalence method figure; Prevalence (Negative Controls) on x-axis against Prevalence (True Samples) on y-axis?

#108 marwa38 closed 2 years ago
7
Methylobacterium-Methylorubrum as a contaminant, advice?

#107 marwa38 closed 2 years ago
3
Where does quant_reading come from? Where does it go?

#106 pauGuas opened 2 years ago
1
Weird decontam performance

#105 Gian77 opened 3 years ago
13