benjjneb/dada2 issues and pull requests

#2051 - trnL through ITS pipeline : variable and sometimes significant loss of sequences upon merging

Issue - State: closed - Opened by jorondo1 16 days ago - 3 comments

#2050 - trimLeft and trimRight documentation?

Issue - State: open - Opened by gerverska 20 days ago - 2 comments

#2049 - Question from DADA2 + PacBio: Fecal samples tuorial

Issue - State: open - Opened by AngusBall 22 days ago

#2048 - The same ASV is coming up in BLAST as a different taxonomy in comparison to when I run qiime feature-classifier classify-sklearn

Issue - State: closed - Opened by ankurnaqib 24 days ago - 2 comments

#2047 - General question about pseudo-pooling

Issue - State: open - Opened by cjfields 26 days ago - 1 comment

#2046 - Assign taxonomy error

Issue - State: open - Opened by DimitraIoli 29 days ago - 3 comments

#2045 - Error estimating error rates and plotting quality profiles

Issue - State: open - Opened by Guillermouceda about 1 month ago - 6 comments

#2044 - DADA2 ITS trimming question

Issue - State: open - Opened by UniAlberta about 1 month ago - 4 comments

#2043 - Dereplication

Issue - State: open - Opened by gabrieltedone about 1 month ago - 1 comment

#2042 - Increase sensitivity towards rare clades

Issue - State: closed - Opened by mgabriell1 about 1 month ago - 2 comments

#2041 - Flat and "gappy" error model for PacBio Revio Kinnex 16S

Issue - State: closed - Opened by mgabriell1 about 1 month ago - 3 comments

#2040 - Training Metazoogene database for dada2

Issue - State: closed - Opened by ClarissaUnderwater about 1 month ago - 1 comment

#2039 - ITS workflow. Problem with primer revoval using cutadapt

Issue - State: open - Opened by Guillermouceda about 1 month ago - 3 comments

#2038 - removeBimeraDenovo taking long time to run with no results

Issue - State: open - Opened by Guillermouceda about 1 month ago

#2037 - filterandTrim step removing >90% of NovaSeq reads

Issue - State: closed - Opened by Anto007 about 1 month ago - 2 comments

#2036 - Merge ASV tables after using trimRight

Issue - State: open - Opened by ma-n-on about 2 months ago - 5 comments

#2035 - why do I find forward primers in forward reads but very few reverse primers in reverse reads (illumina)?

Issue - State: open - Opened by haigthey about 2 months ago - 1 comment

#2034 - Extracting original sequences

Issue - State: open - Opened by SheepwormJM about 2 months ago - 3 comments

#2033 - Combining Runs of Different Quality for Analysis.

Issue - State: open - Opened by DCHed about 2 months ago - 1 comment

#2032 - Creating a DADA2 Error Model from PacBio data with low levels of sequence replication

Issue - State: open - Opened by brandon-osullivan about 2 months ago - 1 comment

#2031 - Workaround options for read loss in filterAndTrim / premerging PE reads / maxEE flag

Issue - State: open - Opened by ThomePauline about 2 months ago - 1 comment

#2030 - Questions about chimera filtering

Issue - State: open - Opened by hjarnek about 2 months ago - 3 comments

#2029 - filterAndTrim returns no reads with least restrictive parameters

Issue - State: closed - Opened by HaigBishop about 2 months ago - 7 comments

#2028 - post-taxonomy assignment issue with data transformation

Issue - State: closed - Opened by TamarKopadze 2 months ago - 1 comment

#2027 - Reads Loss during DADA2 run

Issue - State: closed - Opened by mentorwan 2 months ago - 7 comments

#2026 - assigntaxonomy

Issue - State: open - Opened by UniAlberta 2 months ago - 6 comments

#2025 - Error rates "error"

Issue - State: open - Opened by Kachn42 2 months ago - 3 comments

#2024 - windows-multithread problem (R) - removeBimeraDenovo()

Issue - State: closed - Opened by gianINTERN 2 months ago - 1 comment

#2023 - How does a small database affect the taxonomic assignment?

Issue - State: open - Opened by Fmicro23 2 months ago - 1 comment

#2022 - removeBimeraDenovo not possible to multithread on windows (R)

Issue - State: closed - Opened by gianINTERN 2 months ago - 5 comments

#2021 - Collapsing ASVs into OTUs?

Issue - State: open - Opened by marinachen 2 months ago - 1 comment

#2020 - truncLenKeep

Issue - State: open - Opened by LukeLikesDirt 2 months ago - 3 comments
Labels: enhancement

#2019 - 16S data treatment with very low abundance

Issue - State: open - Opened by karenandreac 2 months ago - 1 comment

#2018 - DADA2 analysis for two different platforms MISEQ and Novaseq -Merging of sequence table

Issue - State: open - Opened by Jayakanthankk 2 months ago - 3 comments

#2017 - Large number of (spurious ?) ASVs Novaseq

Issue - State: open - Opened by msalamon2 3 months ago - 7 comments

#2016 - How to use 16S-ITGDB database in dada2?

Issue - State: closed - Opened by benhardestevao 3 months ago - 1 comment

#2015 - Parameters optimal to produce COI exact variants.

Issue - State: open - Opened by aimirza 3 months ago - 4 comments

#2014 - Formatting RDP version 19 taxonomic database for DADA2

Issue - State: open - Opened by jheiman06 3 months ago - 2 comments
Labels: enhancement, Priority

#2013 - Questions about HiFi filtering process

Issue - State: closed - Opened by mentorwan 3 months ago - 10 comments

#2012 - Merged files, where should I start in the pipeline and how?

Issue - State: open - Opened by seqlt 3 months ago - 2 comments

#2011 - Different Illumina sequencing kits (v2 and v3) - preprocessing

Issue - State: open - Opened by luizastein 3 months ago - 3 comments

#2010 - Large variability in sequence lengths after merging paired reads

Issue - State: open - Opened by alannajmcc16 3 months ago - 1 comment

#2009 - Large amount of losses in read number during processing: PacBio Hifi reads

Issue - State: open - Opened by HitMonk 3 months ago - 4 comments

#2008 - Is filterAndTrim effect to NA results or because minBoot? What parameter setting should be used appropriately?

Issue - State: open - Opened by WP-SMILE 3 months ago - 5 comments

#2007 - filterAndTrim

Issue - State: open - Opened by AliciaBalbin 3 months ago - 1 comment

#2006 - FilterAndTrim discards huge amount of reads with trunclen option

Issue - State: open - Opened by sofiehn 3 months ago - 9 comments

#2005 - learnErrors() on PacBio 16S very slow

Issue - State: open - Opened by trawler-crawler 3 months ago - 8 comments

#2004 - Incertae_sedis VS NA Taxonomic Assignment

Issue - State: open - Opened by mya-darsan 3 months ago - 1 comment

#2003 - about plotQualityProfile and derepFastq function

Issue - State: open - Opened by dstrgcv 3 months ago - 1 comment

#2002 - (Apparent) Negative Phred Scores - Justification

Issue - State: closed - Opened by andrebolerbarros 3 months ago - 2 comments

#2001 - Issue with Primer Removal- Residual Primers After Cutadapt

Issue - State: open - Opened by alannajmcc16 3 months ago - 2 comments

#2000 - How to use cutadapt on merged forward and reverse paired end files? Keep running into errors.

Issue - State: open - Opened by kdbchau 3 months ago - 12 comments

#1999 - 【ERROR】Exception: An error was encountered while running DADA2 in R (return code -11)

Issue - State: open - Opened by AlenaYoung 3 months ago - 1 comment

#1998 - Problem with Taxonomy Assignment DADA2

Issue - State: closed - Opened by TamarKopadze 4 months ago - 7 comments

#1997 - Should you trim samples individually or together?

Issue - State: closed - Opened by hjarnek 4 months ago - 4 comments

#1996 - High number of bimeras/ messy error plots?

Issue - State: open - Opened by brittneybrowning 4 months ago - 2 comments

#1995 - Low diversity in the beginning of the sequence & DADA2 impacts

Issue - State: open - Opened by andrebolerbarros 4 months ago - 3 comments

#1994 - Combining ASV data of same samples from two different run

Issue - State: open - Opened by MizanurRahman24 4 months ago - 5 comments

#1993 - Leptospira species targeting secY gene (instead of 16S) using AmpSeq method?

Issue - State: open - Opened by marwa38 4 months ago - 10 comments

#1992 - Merging two datasets trimmed with different criteria

Issue - State: closed - Opened by andrebolerbarros 4 months ago - 4 comments

#1991 - `fastp` before `dada2`

Issue - State: closed - Opened by andrebolerbarros 4 months ago - 4 comments

#1990 - Error Estimation Issues

Issue - State: open - Opened by adomenig 4 months ago - 6 comments

#1989 - Weird error plots on merged reads

Issue - State: open - Opened by msalamon2 4 months ago - 2 comments

#1988 - quality score plot DADA2

Issue - State: open - Opened by murheisa 4 months ago - 3 comments

#1987 - Error "Can't stage file https://files.plutof.ut.ee:" Download of DADA2 ITS fungi-all fail

Issue - State: open - Opened by himamura2 4 months ago - 3 comments

#1986 - Per Ben's request: Please improve "Assign Taxonomy" Tutorial Language

Issue - State: open - Opened by solangesaxby 4 months ago
Labels: tutorial

#1985 - A theoretically better approach to filtering, trimming & merging?

Issue - State: open - Opened by hjarnek 4 months ago

#1984 - Issue regarding merging data

Issue - State: open - Opened by Aziz4306 4 months ago - 5 comments

#1983 - DADA2-formatted reference database for SILVA 138.2

Issue - State: open - Opened by nr0cinu 4 months ago - 6 comments
Labels: enhancement, Priority

#1982 - indels at ends of DNA sequence

Issue - State: closed - Opened by csmiguel 4 months ago - 2 comments

#1981 - Denoising amplicons from multilocus PCRs

Issue - State: closed - Opened by csmiguel 5 months ago

#1980 - Are these error plots okay?

Issue - State: closed - Opened by biadelbianco 5 months ago - 2 comments

#1979 - error regarding addSpecies and assignSpecies command in DADA2

Issue - State: open - Opened by abhisek061github 5 months ago - 3 comments

#1978 - Primers, cutadapt output and chimera

Issue - State: closed - Opened by luigallucci 5 months ago - 4 comments

#1977 - Pooling, big data and classic tutorial

Issue - State: closed - Opened by luigallucci 5 months ago - 3 comments

#1976 - Is there any way to further speed up dada?

Issue - State: open - Opened by constructivedio 5 months ago - 3 comments

#1975 - When processing full-length 16S data, the ASV table output by makeSequenceTable has an unusually low number of sequences in the sample

Issue - State: open - Opened by M-o-Y-u 5 months ago - 11 comments

#1974 - Using screen background to remove noise with dada2 times error.

Issue - State: open - Opened by GoldLIU 5 months ago - 4 comments

#1973 - Assigning sample names, time points, etc. in phyloseq step

Issue - State: open - Opened by backwards-charm 5 months ago - 3 comments
Labels: documentation

#1972 - The deprecated feature was likely used in the dada2 package.

Issue - State: closed - Opened by sar515 6 months ago - 1 comment

#1971 - Problem with taxa assignation

Issue - State: open - Opened by martina-nasuelli 6 months ago - 3 comments

#1970 - Keeping missing data / Ns in the reads

Issue - State: closed - Opened by ThomePauline 6 months ago - 1 comment

#1969 - ONT error model [question]

Issue - State: closed - Opened by ccrinconc 6 months ago - 2 comments

#1968 - Merging two V4 runs together

Issue - State: open - Opened by MadsBjornsen 6 months ago - 1 comment

#1967 - None of my Lactobacillus genus have been assigned species after using assignTaxonomy. Please assist

Issue - State: closed - Opened by asavelaolona 6 months ago - 2 comments

#1966 - Cluster to OTU, not ASVs?

Issue - State: open - Opened by mya-darsan 6 months ago - 3 comments

#1965 - error laoding the dada2 library

Issue - State: open - Opened by marwa38 6 months ago - 5 comments

#1964 - Add tracking and checking or guidance on what chimera removal method to use based on dada pooling mode

Issue - State: open - Opened by benjjneb 6 months ago
Labels: enhancement

#1963 - DADA2 Error Rate Plots

Issue - State: closed - Opened by goodguynickpt 6 months ago - 16 comments
Labels: support

#1961 - `plotErrors` improvements: Drop zero-observation points and scale points by number of observations

Issue - State: open - Opened by benjjneb 6 months ago - 2 comments
Labels: enhancement

#1960 - Update deprecated tutorials to make their deprecation clear

Issue - State: open - Opened by benjjneb 6 months ago - 1 comment

#1959 - Segmentation fault core dumped on the derep step with Kinnex full length reads

Issue - State: closed - Opened by sbedwell27 6 months ago - 6 comments

GitHub / benjjneb/dada2 issues and pull requests