Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / 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 25 days ago
- 1 comment
Labels: enhancement, Priority
#2013 - Questions about HiFi filtering process
Issue -
State: open - Opened by mentorwan 25 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 26 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
#1930 - garbled fastq files after Filter and trim
Issue -
State: open - Opened by Danyang1111 6 months ago
- 1 comment
#1929 - Problem trimming primers
Issue -
State: open - Opened by Gian77 6 months ago
- 2 comments
#1928 - Loosing reads after merging
Issue -
State: open - Opened by hellewiedunkle 6 months ago
- 5 comments
#1927 - Fecal samples not the same results and error msg when learning errors
Issue -
State: open - Opened by FlorianRocher 6 months ago
- 2 comments
#1926 - computational requirements for running DADA2
Issue -
State: open - Opened by madjus98 6 months ago
- 1 comment
#1925 - reference database for the function AssignTaxonomy()
Issue -
State: open - Opened by madjus98 6 months ago
- 6 comments
#1924 - Error in add(bin) : internal: buf != <newline> in Sample Inference
Issue -
State: closed - Opened by Jiayonglai123 6 months ago
- 2 comments