benjjneb/dada2 issues and pull requests

#1923 - Need helping solving error during inserting a loop of parameters inside the filterandtrim command

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

#1922 - Switch from a phyloseq object to a dada2 object

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

#1921 - nonchim percentage

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

#1920 - Mixed-orientation reads & orient.fwd loses >50% of sequences

Issue - State: open - Opened by sasugden 6 months ago
Labels: support

#1919 - Construct phylogenetic tree error

Issue - State: open - Opened by MiriamFuentesV 6 months ago

#1918 - Half of the bar chart has no data

Issue - State: open - Opened by CatCatcher1 6 months ago - 3 comments

#1917 - 40% of reads survived the pipeline

Issue - State: open - Opened by dsamoht 6 months ago
Labels: support

#1916 - too long in removing chimeras

Issue - State: open - Opened by Karelynz 7 months ago - 1 comment

#1915 - filterAndTrim returns error " 'names' attribute [81] must be the same length as the vector [33]" although fnFs, filtFs, fnRs and filtRs have the same length

Issue - State: open - Opened by jorgeamaya 7 months ago - 1 comment

#1914 - Error: Memory allocation failed.

Issue - State: closed - Opened by acosta91 7 months ago - 9 comments

#1913 - TrnL misassignement using assignTaxonomy with custom database

Issue - State: open - Opened by SarahP4 7 months ago - 4 comments

#1912 - Reporting Pipeline Stats for all samples(not just first 6)

Issue - State: open - Opened by okortenkamp 7 months ago - 1 comment

#1911 - Galaxy tutorial

Issue - State: open - Opened by bernt-matthias 7 months ago

#1910 - depreciated function in plotQualityProfile

Issue - State: closed - Opened by brikw 7 months ago - 1 comment

#1909 - Where in the argument within "filterAndTrim" can I trim the nucleotides with quality score less than 20 ?

Issue - State: open - Opened by mohsamir2023 7 months ago - 7 comments

#1908 - .

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

#1907 - .

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

#1906 - Weird error plot with doubtful taxonomy

Issue - State: open - Opened by Varun9599 7 months ago - 2 comments

#1905 - Need help in using cutadapt to trim paired-end fastq reads to provide as input for DADA2

Issue - State: closed - Opened by akspat 7 months ago - 1 comment

#1904 - adapters 16s

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

#1903 - MergePairs Error

Issue - State: open - Opened by Hellomissgabby 7 months ago - 1 comment

#1902 - Warning in assignTaxonomy() ignoring 1-letter sequences and data not multiple of number of rows

Issue - State: open - Opened by cergare 7 months ago - 1 comment

#1901 - Dereplication timing

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

#1900 - Issue merging reads across sequence runs and diagnosing sequence batch effects PacBio ITS Sequel II samples

Issue - State: open - Opened by dawsonfairbanks 7 months ago - 1 comment
Labels: support

#1899 - Method to get sequences that fail denoising?

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

#1898 - Different number of ASVs

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

#1897 - learnErrors DADA2

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

#1896 - truncQ and maxEE - Archaea 16s V3-V5

Issue - State: closed - Opened by luigallucci 7 months ago - 10 comments

#1895 - ASVs are assigned different when using SILVA 138.1 database versus using NCBI blast

Issue - State: open - Opened by MadsBjornsen 7 months ago - 10 comments

#1894 - Error: vector memory exhausted (limit reached?)

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

#1893 - How to handle Element AVITI data (16S amplicon sequencing)

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

#1892 - PacBio Revio Kinnex data

Issue - State: open - Opened by cjfields 7 months ago - 13 comments
Labels: question

#1891 - EXCTRACTING SST netCDF4 data using Spyder

Issue - State: open - Opened by hadeerIsmail22 8 months ago

#1890 - Filter and trim error (dada2)

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

#1889 - Dual amplicon processing and filtering

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

#1888 - Demultiplex error

Issue - State: open - Opened by Hellomissgabby 8 months ago - 7 comments

#1887 - inconsistent "invalid DNAString input character" errors

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

#1886 - Graceful handling of zero-length reads?

Issue - State: open - Opened by Danyang1111 8 months ago - 3 comments
Labels: bug

#1885 - questions of Dereplication

Issue - State: open - Opened by Danyang1111 8 months ago - 5 comments

#1884 - TruncQ parameter not correlating with reads out

Issue - State: open - Opened by chung-wingko 8 months ago - 1 comment

#1883 - problem with Sample Inference

Issue - State: open - Opened by Danyang1111 8 months ago - 1 comment

#1882 - Pacbio HiFi long time at learnErrors + other issues.

Issue - State: closed - Opened by nathanjohns 8 months ago - 2 comments

#1881 - PR2 5.0.0 Release AssignTaxonomy Function Timing

Issue - State: open - Opened by margaret-rettig 8 months ago - 4 comments

#1880 - Single orientation asv in mixed orientation amplicon library?

Issue - State: closed - Opened by DollyPrrrton 8 months ago - 2 comments

#1879 - dada2 packbio and cutadapt

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

#1878 - Inconsistent Data Loss in Replicated DADA2 Runs with Identical Parameters

Issue - State: open - Opened by saharbagheri 9 months ago - 2 comments

#1877 - Processing time for dada() with PacBio reads

Issue - State: open - Opened by HeiserS 9 months ago - 4 comments

#1876 - Crash and reboot when using DADA2 with PR2

Issue - State: open - Opened by ThibauldMichel 9 months ago - 2 comments

#1875 - One sample versus multiple samples

Issue - State: open - Opened by NextGenSeek 9 months ago - 1 comment

#1874 - Issue with using cutadapt in R on a Windows system

Issue - State: closed - Opened by gemwalker 9 months ago - 1 comment

#1873 - Pull rep seqs for ASVs without taxonomy

Issue - State: open - Opened by aron1014 9 months ago - 2 comments

#1872 - mergePairs error

Issue - State: closed - Opened by bdonnelly112493 9 months ago

#1871 - Optimizing filterAndTrim settings for different datasets (ITS2) when quality scores differ

Issue - State: open - Opened by ekronold 9 months ago - 2 comments

#1870 - All the rows of seqtab.nochim are NA

Issue - State: closed - Opened by radhiasdf 9 months ago - 1 comment

#1869 - Cutadapt leaving a set of primers

Issue - State: open - Opened by Jiayonglai123 9 months ago - 5 comments

#1868 - Getting Error When assigning taxonomy in R

Issue - State: closed - Opened by wangz14 9 months ago - 8 comments

#1867 - Greengenes2 reference database for DADA2 using R

Issue - State: open - Opened by mutjangee 9 months ago - 1 comment

#1866 - Reads loss during nonchim step.

Issue - State: open - Opened by hh1985 10 months ago - 1 comment

#1865 - Large ammount of ASVs and large amount of read loss during chimera removal

Issue - State: open - Opened by robbueck 10 months ago - 3 comments

#1864 - Allowing "justconcatenate = TRUE" to minimize loss of much reads during merging stage

Issue - State: open - Opened by biazen123 10 months ago - 7 comments

#1863 - error with FilterAndTrim names

Issue - State: open - Opened by miguelsemedobb 10 months ago - 3 comments

#1862 - Error in getting species level

Issue - State: open - Opened by deepan-design 10 months ago - 1 comment

#1861 - Removing primers error: Error in sum(hits.fwd) : invalid 'type' (list) of argument

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

#1860 - Error when merging paired end reads

Issue - State: open - Opened by bdonnelly112493 10 months ago - 2 comments

#1859 - Couldn't automatically detect the sequence identifier field in the fastq id string

Issue - State: closed - Opened by wygbio 10 months ago - 2 comments

#1858 - I get the following Errors when I run Cutadapt in R studio environment based on the tutorial scripts. The subdirectory folder cutadapt was created but no files. I am not clear on it, please can you help me how can I solve it,

Issue - State: closed - Opened by biazen123 10 months ago - 1 comment

#1857 - Losing a high percentage of reads after merging AND after chimeras removal.

Issue - State: open - Opened by NoGaud 10 months ago - 8 comments

#1856 - Can DADA2 pipeline process MinION ITS1 and ITS2 single read fastq files?

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

#1855 - LearnErrors fail

Issue - State: open - Opened by najouamghazli 10 months ago - 3 comments

#1854 - SRFilterResult error

Issue - State: open - Opened by Laurco7 10 months ago - 1 comment

#1853 - Question regarding the computation of the p-value

Issue - State: closed - Opened by pereiramemo 11 months ago - 5 comments

#1852 - new PR2 database levels

Pull Request - State: closed - Opened by leholman 11 months ago

#1851 - Error: BiocParallel errors 1 remote errors, element index: 1 0 unevaluated and other errors first remote error:

Issue - State: closed - Opened by marwa38 11 months ago - 17 comments

#1850 - Errors with learnErrors -related to new R version?

Issue - State: open - Opened by cchen1 11 months ago - 1 comment

#1849 - Error rates could not be estimated (this is usually because of very few reads). Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.

Issue - State: open - Opened by harleenkchaggar 11 months ago - 4 comments

#1848 - A 20bps GAP in merged reads' length distribution.

Issue - State: open - Opened by gabrieltedone 11 months ago - 1 comment

#1847 - plot quality error Error in UseMethod("depth") : no applicable method for 'depth' applied to an object of class "NULL"

Issue - State: open - Opened by murheisa 11 months ago - 1 comment

#1846 - No generated files after using Cutadapt in DADA2 analysis for ITS

Issue - State: closed - Opened by darjniki 11 months ago - 8 comments

#1845 - How to determine the truncation length based on binned quality score profile?

Issue - State: open - Opened by chenyj8 11 months ago - 1 comment

#1844 - plotQualityProfile

Issue - State: open - Opened by avportal 11 months ago

#1843 - merging replicates of sequences using DADA2 and Phyloseq

Issue - State: open - Opened by Abdy83 11 months ago - 1 comment

#1842 - Using dada2 to process single sample fasta files

Issue - State: open - Opened by rowe285 11 months ago - 2 comments

#1841 - mergeSequenceTables library normalization

Issue - State: closed - Opened by nikoladaskova 11 months ago - 1 comment

#1840 - Output of Full Sequences from Assign Taxonomy

Issue - State: open - Opened by rmassoni16 11 months ago - 1 comment

#1839 - DADA2 denoise of PacBio sequences produced Warning: NAs produced by integer overflow

Issue - State: open - Opened by emankhalaf 11 months ago - 7 comments

#1838 - Missing sequence for record beginning on line 69721

Issue - State: open - Opened by adevries75 12 months ago - 4 comments

#1837 - exporting sequences after the removal of the chimeras

Issue - State: open - Opened by sluitgaarden 12 months ago - 5 comments

#1836 - 16S rRNA pipeline using DADA2 /Construct Phylogenetic Tree

Issue - State: open - Opened by MostafaShaban989 12 months ago - 1 comment

#1835 - 16S rRNA pipeline using DADA2 / 10. Alignment

Issue - State: closed - Opened by MostafaShaban989 12 months ago - 2 comments

#1834 - Error in reading fastq file

Issue - State: open - Opened by apcristi 12 months ago - 1 comment

#1833 - How to merge fastq files from NCBI to my data

Issue - State: closed - Opened by AkilaMuthalagu 12 months ago - 4 comments

#1832 - Losing >50% of Reads on Merge

Issue - State: open - Opened by D-gallinson 12 months ago - 2 comments

#1831 - Taxa assignment fail

Issue - State: closed - Opened by luisymbio 12 months ago - 2 comments

#1830 - Merging two different runs may reflect in a samples separation in a downstream ordination?

Issue - State: closed - Opened by MatS792 12 months ago - 6 comments

#1829 - Greengenes2 database not through qiime2

Issue - State: closed - Opened by lcamVz 12 months ago - 2 comments
Labels: enhancement, Priority

GitHub / benjjneb/dada2 issues and pull requests