benjjneb/dada2 issues and pull requests

#1863 - error with FilterAndTrim names

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

#1862 - Error in getting species level

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

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

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

#1860 - Error when merging paired end reads

Issue - State: open - Opened by bdonnelly112493 12 months ago - 2 comments

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

Issue - State: closed - Opened by wygbio 12 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 12 months ago - 1 comment

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

Issue - State: open - Opened by NoGaud almost 1 year ago - 8 comments

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

Issue - State: open - Opened by Noor-Deen about 1 year ago - 4 comments

#1855 - LearnErrors fail

Issue - State: open - Opened by najouamghazli about 1 year ago - 3 comments

#1854 - SRFilterResult error

Issue - State: open - Opened by Laurco7 about 1 year ago - 1 comment

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

Issue - State: closed - Opened by pereiramemo about 1 year ago - 5 comments

#1852 - new PR2 database levels

Pull Request - State: closed - Opened by leholman about 1 year 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 about 1 year ago - 17 comments

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

Issue - State: open - Opened by cchen1 about 1 year 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 about 1 year ago - 4 comments

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

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

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

Issue - State: closed - Opened by darjniki about 1 year ago - 8 comments

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

Issue - State: open - Opened by chenyj8 about 1 year ago - 1 comment

#1844 - plotQualityProfile

Issue - State: open - Opened by avportal about 1 year ago

#1843 - merging replicates of sequences using DADA2 and Phyloseq

Issue - State: open - Opened by Abdy83 about 1 year ago - 1 comment

#1842 - Using dada2 to process single sample fasta files

Issue - State: open - Opened by rowe285 about 1 year ago - 2 comments

#1841 - mergeSequenceTables library normalization

Issue - State: closed - Opened by nikoladaskova about 1 year ago - 1 comment

#1840 - Output of Full Sequences from Assign Taxonomy

Issue - State: open - Opened by rmassoni16 about 1 year ago - 1 comment

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

Issue - State: open - Opened by emankhalaf about 1 year ago - 7 comments

#1838 - Missing sequence for record beginning on line 69721

Issue - State: open - Opened by adevries75 about 1 year ago - 4 comments

#1837 - exporting sequences after the removal of the chimeras

Issue - State: open - Opened by sluitgaarden about 1 year ago - 5 comments

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

Issue - State: open - Opened by MostafaShaban989 about 1 year ago - 1 comment

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

Issue - State: closed - Opened by MostafaShaban989 about 1 year ago - 2 comments

#1834 - Error in reading fastq file

Issue - State: open - Opened by apcristi about 1 year ago - 1 comment

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

Issue - State: closed - Opened by AkilaMuthalagu about 1 year ago - 4 comments

#1832 - Losing >50% of Reads on Merge

Issue - State: open - Opened by D-gallinson about 1 year ago - 2 comments

#1831 - Taxa assignment fail

Issue - State: closed - Opened by luisymbio about 1 year ago - 2 comments

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

Issue - State: closed - Opened by MatS792 about 1 year ago - 6 comments

#1829 - Greengenes2 database not through qiime2

Issue - State: closed - Opened by lcamVz about 1 year ago - 2 comments
Labels: enhancement, Priority

#1828 - % of chimera detected seems too high

Issue - State: open - Opened by AnaMariaCabello about 1 year ago - 2 comments

#1827 - Addspecies() doesn't add any species

Issue - State: closed - Opened by WJH58 about 1 year ago - 2 comments

#1826 - Converting DADA2 results to a standard OTU table

Issue - State: closed - Opened by hwangumn about 1 year ago - 1 comment

#1825 - Denoise step still running after 10 days

Issue - State: open - Opened by magibc about 1 year ago - 3 comments

#1824 - ackage

Issue - State: closed - Opened by FloMazel about 1 year ago

#1823 - FilterAndTrim for ITS sequences

Issue - State: open - Opened by hwangumn about 1 year ago - 3 comments

#1822 - Missing Taxonomy

Issue - State: open - Opened by mycojon about 1 year ago - 4 comments

#1821 - Availability of Greengenes2 database in DADA2 pipeline

Issue - State: closed - Opened by magibc about 1 year ago - 2 comments

#1820 - Issue with primer removal step

Issue - State: open - Opened by anamariamunizrodriguez about 1 year ago - 2 comments

#1819 - Single fasta file containing all samples and requences into a usable format for dada2 analysis

Issue - State: open - Opened by anamariamunizrodriguez about 1 year ago - 2 comments

#1818 - DADA2 stand alone output and LotuS2 - DADA2 produces different outcomes

Issue - State: open - Opened by Balaveer about 1 year ago - 2 comments

#1817 - assignTaxonomy function returned results that are mostly NA

Issue - State: open - Opened by Canxis about 1 year ago - 2 comments

#1816 - Cutadapt removal of primer

Issue - State: open - Opened by luisymbio about 1 year ago - 6 comments

#1815 - issue with qiime dada2 denoise-ccs

Issue - State: open - Opened by daisykuma22 about 1 year ago - 1 comment

#1814 - seqtab.rds to .fasta with sample names

Issue - State: closed - Opened by LukeLikesDirt about 1 year ago - 2 comments

#1813 - Filtering Phyla that have low feature prevalence

Issue - State: open - Opened by Ecotone23 about 1 year ago - 8 comments

#1812 - parallelization in filterAndTrim for Window OS

Pull Request - State: open - Opened by cylyau about 1 year ago

#1811 - Remove a cycle without discarding reads

Issue - State: open - Opened by ajaltomare about 1 year ago - 3 comments

#1810 - Parallelization with dada2 big data workflow

Issue - State: closed - Opened by luisymbio about 1 year ago - 4 comments

#1809 - Aborted R session with DADA2 run for a large number of PacBio-sequenced samples

Issue - State: open - Opened by emankhalaf about 1 year ago - 11 comments

#1808 - How long does it take for R to assign fungal taxonomies?

Issue - State: closed - Opened by LordoftheMelons about 1 year ago - 4 comments

#1807 - Removing primers with trimLeft

Issue - State: open - Opened by nuorenarra about 1 year ago - 2 comments

#1806 - The lengths are different between dereps an dadas

Issue - State: open - Opened by suzywang116 over 1 year ago - 10 comments

#1805 - Error in is(obj, "matrix") : object 'errF' not found

Issue - State: open - Opened by KOMALSKK over 1 year ago - 3 comments

#1804 - errf

Issue - State: open - Opened by KOMALSKK over 1 year ago

#1803 - denoise-ccs for ITS

Issue - State: open - Opened by Hobgoblin8 over 1 year ago - 1 comment

#1802 - Losing reads after removing chimera

Issue - State: closed - Opened by osidaksjdmw over 1 year ago - 2 comments

#1801 - ggplot2 issue

Issue - State: closed - Opened by nstrom1 over 1 year ago - 1 comment

#1800 - asigntaxonomy command and taxlevels argument

Issue - State: open - Opened by Guillermouceda over 1 year ago - 3 comments

#1799 - Problem after removing chimera steps

Issue - State: closed - Opened by sskoldas over 1 year ago - 4 comments

#1798 - PacBio 16S sequence-reg

Issue - State: open - Opened by Balakulandai over 1 year ago - 1 comment

#1797 - Filter plants contigs after dada2 ITS workflow

Issue - State: closed - Opened by laisoemis over 1 year ago - 1 comment

#1796 - Error with taxonomic assignment in 16s analysis

Issue - State: closed - Opened by Sada-mwatelah over 1 year ago - 2 comments

#1795 - ITS filterAndTrim: No reads passed the filter + Denoising Errors dadaFs/Rs <- dada()

Issue - State: open - Opened by jordan-dwm over 1 year ago - 2 comments

#1794 - errF <- learnErrors

Issue - State: closed - Opened by genesandbones over 1 year ago - 2 comments

#1793 - error loading quality score plots

Issue - State: open - Opened by sophiasaleki over 1 year ago - 1 comment

#1792 - Error in removeBimeraDenovo

Issue - State: open - Opened by JulianMiGoe over 1 year ago - 10 comments

#1791 - Trimming Suggestion for 16S V3

Issue - State: closed - Opened by Jiayonglai123 over 1 year ago - 4 comments

#1790 - DADA2: Filtering and Trimming

Issue - State: open - Opened by Lightcrane-h over 1 year ago - 1 comment

#1789 - Combining ASV feature table and taxonomy table?

Issue - State: closed - Opened by skose82 over 1 year ago - 2 comments

#1788 - (DADA ITS) Error in filterAndTrim(cutFs, filtFs, cutRs, filtRs, maxN = 0, maxEE = c(2, :

Issue - State: closed - Opened by Parikrama over 1 year ago - 9 comments

#1787 - (ITS DADA2) Error in rval[sapply(rval, is.character)] : invalid subscript type 'list'

Issue - State: open - Opened by Parikrama over 1 year ago - 14 comments

#1786 - why do i have empty ASVs after running the dada function?

Issue - State: closed - Opened by gabrielet over 1 year ago - 2 comments

#1785 - % similarity against best match for each ASV

Issue - State: open - Opened by Paoluxxe over 1 year ago - 3 comments

#1784 - zero unclassified taxa at genus level?

Issue - State: open - Opened by gabrielet over 1 year ago - 1 comment

#1783 - Making a custom LSU database with DADA2 from Silva files

Issue - State: open - Opened by JFranklin5221 over 1 year ago - 6 comments

#1782 - DADA2 makeTaxonomyFasta_SilvaNR

Issue - State: closed - Opened by JFranklin5221 over 1 year ago

#1781 - Missing samples in bar plot

Issue - State: open - Opened by arna3 over 1 year ago - 12 comments

#1780 - Error models and ASV detection

Issue - State: closed - Opened by zinfin over 1 year ago - 1 comment

#1779 - 18S workflow in DADA2 issue：Error in h(simpleError(msg, call)) : Error evaluating 'x' parameter when selecting method for 'reverseComplement' function: key 70 (char 'F') not in lookup table

Issue - State: open - Opened by hehanhhh over 1 year ago - 5 comments

#1778 - memory leak during learnErrors

Issue - State: open - Opened by Adwyness over 1 year ago - 1 comment

#1777 - OTUs from V4 region of 16S rRNA assigned as eukaryota

Issue - State: open - Opened by Ecotone23 over 1 year ago - 4 comments

#1776 - Question about merged read for assigning taxonomy by dada2 package in R

Issue - State: open - Opened by chengcheng0625 over 1 year ago - 4 comments

#1775 - Question about reverse complement in assignTaxonomy

Issue - State: open - Opened by mtsiknia over 1 year ago - 2 comments

#1774 - Dealing with Variable Sequence Lengths in DADA2

Issue - State: open - Opened by alexandriai168 over 1 year ago - 1 comment

#1773 - Too many ASVs in mock community

Issue - State: open - Opened by rachel-1212 over 1 year ago - 2 comments

#1772 - Loosing alot of reads

Issue - State: open - Opened by MadsBjornsen over 1 year ago - 5 comments

#1771 - The number of ASVs is small, the data efficiency is low, and high-abundance sequences are filtered out.

Issue - State: closed - Opened by zhangjl-work over 1 year ago

#1770 - Issue with taxa assignment using custom database

Issue - State: open - Opened by MGMarine over 1 year ago - 7 comments

#1769 - 16S V4 region frequently occurring sequences at start of R1 and R2

Issue - State: open - Opened by johannalheureux23 over 1 year ago - 6 comments

GitHub / benjjneb/dada2 issues and pull requests