benjjneb/dada2 issues and pull requests

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

Issue - State: closed - Opened by gianINTERN 12 days ago - 1 comment

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

Issue - State: open - Opened by Fmicro23 13 days ago - 1 comment

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

Issue - State: closed - Opened by gianINTERN 14 days ago - 5 comments

#2021 - Collapsing ASVs into OTUs?

Issue - State: open - Opened by marinachen 14 days ago - 1 comment

#2020 - truncLenKeep

Issue - State: open - Opened by LukeLikesDirt 16 days ago - 2 comments

#2019 - 16S data treatment with very low abundance

Issue - State: open - Opened by karenandreac 18 days ago - 1 comment

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

Issue - State: open - Opened by Jayakanthankk 18 days ago - 1 comment

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

Issue - State: open - Opened by msalamon2 18 days ago - 3 comments

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

Issue - State: closed - Opened by benhardestevao 20 days ago - 1 comment

#2015 - Parameters optimal to produce COI exact variants.

Issue - State: open - Opened by aimirza 20 days ago - 4 comments

#2014 - Formatting RDP version 19 taxonomic database for DADA2

Issue - State: open - Opened by jheiman06 26 days ago - 1 comment
Labels: enhancement, Priority

#2013 - Questions about HiFi filtering process

Issue - State: open - Opened by mentorwan 26 days ago - 9 comments

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

Issue - State: open - Opened by seqlt 26 days ago - 2 comments

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

Issue - State: open - Opened by luizastein 27 days ago - 3 comments

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

Issue - State: open - Opened by alannajmcc16 28 days ago - 1 comment

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

Issue - State: open - Opened by HitMonk about 1 month ago - 2 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 about 1 month ago - 5 comments

#2007 - filterAndTrim

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

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

Issue - State: open - Opened by sofiehn about 1 month ago - 9 comments

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

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

#2004 - Incertae_sedis VS NA Taxonomic Assignment

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

#2003 - about plotQualityProfile and derepFastq function

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

#2002 - (Apparent) Negative Phred Scores - Justification

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

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

Issue - State: open - Opened by alannajmcc16 about 2 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 about 2 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 about 2 months ago - 1 comment

#1998 - Problem with Taxonomy Assignment DADA2

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

#1997 - Should you trim samples individually or together?

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

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

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

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

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

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

Issue - State: open - Opened by MizanurRahman24 2 months ago - 5 comments

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

Issue - State: open - Opened by marwa38 2 months ago - 10 comments

#1992 - Merging two datasets trimmed with different criteria

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

#1991 - `fastp` before `dada2`

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

#1990 - Error Estimation Issues

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

#1989 - Weird error plots on merged reads

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

#1988 - quality score plot DADA2

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

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

Issue - State: open - Opened by solangesaxby 2 months ago
Labels: tutorial

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

Issue - State: open - Opened by hjarnek 2 months ago

#1984 - Issue regarding merging data

Issue - State: open - Opened by Aziz4306 2 months ago - 5 comments

#1983 - DADA2-formatted reference database for SILVA 138.2

Issue - State: open - Opened by nr0cinu 3 months ago - 3 comments
Labels: enhancement, Priority

#1982 - indels at ends of DNA sequence

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

#1981 - Denoising amplicons from multilocus PCRs

Issue - State: closed - Opened by csmiguel 3 months ago

#1980 - Are these error plots okay?

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

#1979 - error regarding addSpecies and assignSpecies command in DADA2

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

#1978 - Primers, cutadapt output and chimera

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

#1977 - Pooling, big data and classic tutorial

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

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

Issue - State: open - Opened by constructivedio 3 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 3 months ago - 11 comments

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

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

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

Issue - State: open - Opened by backwards-charm 4 months ago - 3 comments
Labels: documentation

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

Issue - State: closed - Opened by sar515 4 months ago - 1 comment

#1971 - Problem with taxa assignation

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

#1970 - Keeping missing data / Ns in the reads

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

#1969 - ONT error model [question]

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

#1968 - Merging two V4 runs together

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

#1966 - Cluster to OTU, not ASVs?

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

#1965 - error laoding the dada2 library

Issue - State: open - Opened by marwa38 4 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 4 months ago
Labels: enhancement

#1963 - DADA2 Error Rate Plots

Issue - State: closed - Opened by goodguynickpt 4 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 4 months ago - 2 comments
Labels: enhancement

#1960 - Update deprecated tutorials to make their deprecation clear

Issue - State: open - Opened by benjjneb 4 months ago - 1 comment

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

Issue - State: closed - Opened by sbedwell27 5 months ago - 6 comments

#1958 - Is it possible to get ASVs with zero counts in all samples after DADA2 run?

Issue - State: closed - Opened by Anto007 5 months ago - 4 comments

#1957 - High chimera rate: +80%

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

#1956 - R session gets aborted during dereplication of reverse reads

Issue - State: closed - Opened by Reeshma01 5 months ago - 1 comment

#1955 - Unexpected results after cutadapt

Issue - State: closed - Opened by jesika0123 5 months ago - 4 comments

#1954 - derep

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

#1953 - Trimming/ derep error

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

#1952 - Is denoising required for kraken analysis?

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

#1951 - Suspiciously high number of low-abundance ASVs (10s of 1000s)?

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

#1950 - Cluster ASVs to OTUs with DECIPHER

Issue - State: closed - Opened by Danyang1111 5 months ago - 3 comments

#1949 - cutadapt: error: cutadapt not able to trim the desired adaptor

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

#1948 - quality filter: imbalance forward vs reverse reads - dada2-

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

#1947 - Increasing number of nonchimeric reads compared to the number of input reads

Issue - State: open - Opened by Abdelrahim-maker 5 months ago - 8 comments

#1946 - Solving the "Error: BiocParallel errors" (in almost every sample)

Issue - State: closed - Opened by Yoonseopark02 5 months ago - 5 comments

#1945 - Solving the "Error: BiocParallel errors", in almost every sample analysis

Issue - State: closed - Opened by Yoonseopark02 5 months ago

#1944 - Clustering dada2-obtained ASVs into OTUs with DECIPHER

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

#1943 - dada2 reference database for eukaryotes

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

#1942 - Differences in chimera detection based on dataset structure

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

#1941 - error: no input files found from Assign taxonomy

Issue - State: open - Opened by bylee613 5 months ago - 5 comments

#1940 - BiocParallel error

Issue - State: open - Opened by ThibauldMichel 5 months ago - 5 comments

#1939 - Number of ASVs changes on different computers/R versions?

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

#1938 - Taxonomy assignment

Issue - State: open - Opened by SRC151 5 months ago - 4 comments

#1937 - Non-fitting Error Plots

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

#1936 - Quality plot profile refence for filterAndTrim truncLen values

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

#1935 - Drop in Qualityscore in the middle of the reads

Issue - State: closed - Opened by MadsBjornsen 5 months ago - 9 comments

#1934 - Don't know if singletons are being removed or not

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

#1933 - Missing reads when transitioning from Dada2 to phyloseq

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

#1932 - Memory error in AssignTaxonomy when working with very small sequences

Issue - State: open - Opened by nearinj 5 months ago - 1 comment
Labels: bug

#1931 - AIUTO file parsing

Issue - State: closed - Opened by chiaragiovannetti11111 5 months ago - 1 comment

GitHub / benjjneb/dada2 issues and pull requests