Ecosyste.ms: Issues

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GitHub / benjjneb/dada2 issues and pull requests

#2080 - Should you create one error model per marker gene?

Issue - State: open - Opened by hjarnek 4 days ago - 4 comments

#2078 - filterAndTrim with ITS data

Issue - State: open - Opened by mya-darsan 15 days ago - 1 comment

#2077 - Compatibility of DADA2 for ITS amplicon reads

Issue - State: open - Opened by UniAlberta 18 days ago - 2 comments

#2072 - What do the filtN files do?

Issue - State: open - Opened by kdbchau 30 days ago - 7 comments

#2070 - missing upper taxonomic rank although genus/species are detected in SILVA 138.

Issue - State: closed - Opened by marwa38 about 1 month ago - 9 comments

#2069 - assignTaxonomic() never ends with UNITE reference dataset

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

#2068 - Verifying presence and orientation of ITS primers

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

#2066 - Problem with long vectors using Pacbio long reads

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

#2064 - How long does assigntTaxonomoy takes with UNITE database?

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

#2063 - Take too long time to runing Taxonomy using UNITE database

Issue - State: open - Opened by Danyang1111 2 months ago - 2 comments

#2061 - Running DADA2 on clusters with pool option -- run of memory

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

#2060 - Should I trim the primers for dada2 workflow?

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

#2059 - question about using derepFastq function

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

#2058 - Long Run Time for Qiime DADA2 Paired-End Denoising

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

#2057 - error with fastqFilter function

Issue - State: closed - Opened by manuelzc 3 months ago - 3 comments

#2056 - running the pipeline with reverse reads only (only R2 available)?

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

#2054 - nbases argument ignored?

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

#2053 - SILVA release 138.2

Issue - State: closed - Opened by ep142 3 months ago - 9 comments

#2052 - DADA2 Error Rate Plots - is this okay?

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

#2050 - trimLeft and trimRight documentation?

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

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

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

#2047 - General question about pseudo-pooling

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

#2046 - Assign taxonomy error

Issue - State: closed - Opened by DimitraIoli 3 months ago - 3 comments

#2045 - Error estimating error rates and plotting quality profiles

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

#2044 - DADA2 ITS trimming question

Issue - State: open - Opened by UniAlberta 4 months ago - 4 comments

#2043 - Dereplication

Issue - State: closed - Opened by gabrieltedone 4 months ago - 1 comment

#2042 - Increase sensitivity towards rare clades

Issue - State: closed - Opened by mgabriell1 4 months ago - 2 comments

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

Issue - State: closed - Opened by mgabriell1 4 months ago - 4 comments

#2040 - Training Metazoogene database for dada2

Issue - State: closed - Opened by ClarissaUnderwater 4 months ago - 1 comment

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

Issue - State: closed - Opened by Guillermouceda 4 months ago - 3 comments

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

Issue - State: closed - Opened by Anto007 4 months ago - 2 comments

#2036 - Merge ASV tables after using trimRight

Issue - State: closed - Opened by ma-n-on 4 months ago - 5 comments

#2034 - Extracting original sequences

Issue - State: closed - Opened by SheepwormJM 4 months ago - 3 comments

#2033 - Combining Runs of Different Quality for Analysis.

Issue - State: closed - Opened by DCHed 4 months ago - 1 comment

#2030 - Questions about chimera filtering

Issue - State: closed - Opened by hjarnek 4 months ago - 3 comments

#2029 - filterAndTrim returns no reads with least restrictive parameters

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

#2028 - post-taxonomy assignment issue with data transformation

Issue - State: closed - Opened by TamarKopadze 4 months ago - 1 comment

#2027 - Reads Loss during DADA2 run

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

#2026 - assigntaxonomy

Issue - State: closed - Opened by UniAlberta 5 months ago - 6 comments

#2025 - Error rates "error"

Issue - State: closed - Opened by Kachn42 5 months ago - 3 comments

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

Issue - State: closed - Opened by gianINTERN 5 months ago - 1 comment

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

Issue - State: open - Opened by Fmicro23 5 months ago - 1 comment

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

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

#2021 - Collapsing ASVs into OTUs?

Issue - State: closed - Opened by marinachen 5 months ago - 1 comment

#2020 - truncLenKeep

Issue - State: open - Opened by LukeLikesDirt 5 months ago - 3 comments
Labels: enhancement

#2019 - 16S data treatment with very low abundance

Issue - State: closed - Opened by karenandreac 5 months ago - 1 comment

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

Issue - State: closed - Opened by msalamon2 5 months ago - 7 comments

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

Issue - State: closed - Opened by benhardestevao 5 months ago - 1 comment

#2015 - Parameters optimal to produce COI exact variants.

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

#2014 - Formatting RDP version 19 taxonomic database for DADA2

Issue - State: closed - Opened by jheiman06 5 months ago - 3 comments
Labels: enhancement, Priority

#2013 - Questions about HiFi filtering process

Issue - State: closed - Opened by mentorwan 5 months ago - 10 comments

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

Issue - State: open - Opened by seqlt 5 months ago - 2 comments

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

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

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

Issue - State: open - Opened by alannajmcc16 5 months ago - 1 comment

#2007 - filterAndTrim

Issue - State: open - Opened by AliciaBalbin 5 months ago - 1 comment

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

Issue - State: open - Opened by sofiehn 6 months ago - 9 comments

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

Issue - State: open - Opened by trawler-crawler 6 months ago - 8 comments

#2004 - Incertae_sedis VS NA Taxonomic Assignment

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

#2003 - about plotQualityProfile and derepFastq function

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

#2002 - (Apparent) Negative Phred Scores - Justification

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

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

Issue - State: open - Opened by alannajmcc16 6 months ago - 2 comments

#1998 - Problem with Taxonomy Assignment DADA2

Issue - State: closed - Opened by TamarKopadze 6 months ago - 7 comments

#1997 - Should you trim samples individually or together?

Issue - State: closed - Opened by hjarnek 6 months ago - 4 comments

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

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

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

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

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

Issue - State: open - Opened by MizanurRahman24 6 months ago - 5 comments

#1992 - Merging two datasets trimmed with different criteria

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

#1991 - `fastp` before `dada2`

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

#1990 - Error Estimation Issues

Issue - State: open - Opened by adomenig 7 months ago - 6 comments

#1989 - Weird error plots on merged reads

Issue - State: open - Opened by msalamon2 7 months ago - 2 comments

#1988 - quality score plot DADA2

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

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

Issue - State: open - Opened by solangesaxby 7 months ago
Labels: tutorial

#1984 - Issue regarding merging data

Issue - State: open - Opened by Aziz4306 7 months ago - 5 comments

#1983 - DADA2-formatted reference database for SILVA 138.2

Issue - State: closed - Opened by nr0cinu 7 months ago - 18 comments
Labels: enhancement, Priority

#1982 - indels at ends of DNA sequence

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

#1981 - Denoising amplicons from multilocus PCRs

Issue - State: closed - Opened by csmiguel 7 months ago