Ecosyste.ms: Issues

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GitHub / benjjneb/dada2 issues and pull requests

#1729 - DADA2 Trimming Parameter Automation

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

#1711 - problem with mergePairs

Issue - State: closed - Opened by cabraham03 over 1 year ago - 2 comments

#1680 - Updated GreenGenes database formatting for DADA2

Issue - State: open - Opened by cfrancoeur almost 2 years ago - 23 comments
Labels: enhancement, Priority

#1674 - DNBseq takes forever to run

Issue - State: open - Opened by thecrobe almost 2 years ago - 4 comments

#1659 - Error with derepFastq

Issue - State: open - Opened by ChristinaOvergaard almost 2 years ago - 5 comments

#1656 - Filtering and trimming dada2

Issue - State: open - Opened by MathildeJqt almost 2 years ago - 3 comments

#1652 - Run DADA2 for multiple studies

Issue - State: open - Opened by ghost almost 2 years ago - 3 comments

#1645 - learnErrors, dada and removeBimeraDenovo result in ‘caught segfault’ error

Issue - State: open - Opened by petrijp almost 2 years ago - 14 comments

#1628 - creating a reference DB to assign taxonomy in Dada2

Issue - State: open - Opened by mycotonia3 about 2 years ago - 11 comments

#1619 - converting a fasta database to dada2 assignTaxonomy format

Issue - State: closed - Opened by soluna1 about 2 years ago - 4 comments

#1612 - unite database assignment of host sequences

Issue - State: open - Opened by connor-morozumi about 2 years ago - 12 comments
Labels: documentation

#1609 - removeBimera never ending

Issue - State: closed - Opened by ChloePZS about 2 years ago - 13 comments

#1526 - Custom Taxonomy Training Set

Issue - State: closed - Opened by RFlazcano over 2 years ago - 6 comments

#1523 - Error in readBin(con, raw(), n) : error reading from the connection

Issue - State: open - Opened by ninglinwang over 2 years ago - 6 comments

#1520 - dada2 pipeline for metabarcoding

Issue - State: closed - Opened by safiqu over 2 years ago - 9 comments

#1464 - Loss of many reads in Reverse and merger steps

Issue - State: closed - Opened by sarah-mangum almost 3 years ago - 8 comments

#1456 - Issues with data frame making

Issue - State: open - Opened by AkilaMuthalagu almost 3 years ago - 6 comments

#1421 - Error in getUniques(x) when running sapply(dadaFs, getN)

Issue - State: closed - Opened by tamerhage about 3 years ago - 5 comments

#1404 - Problems with install DADA2 in R version 4.1

Issue - State: open - Opened by Alejandra31pucv about 3 years ago - 18 comments

#1376 - Non-zero exit status.

Issue - State: closed - Opened by edmundtayzy over 3 years ago - 1 comment

#1375 - Support for Apple M1 arch64

Issue - State: closed - Opened by akhst7 over 3 years ago - 8 comments

#1374 - Is it valid to calculate Good's coverage for DADA2 output ?

Issue - State: closed - Opened by ShailNair over 3 years ago - 2 comments

#1373 - Possible to show 'top 3' taxonomy assignments?

Issue - State: closed - Opened by eefj33 over 3 years ago - 1 comment

#1371 - converting multi-level taxonomy of OTUs to 7-level taxonomy

Issue - State: closed - Opened by alinawazfcc over 3 years ago - 1 comment

#1368 - Remove chimeras, consensus vs. pooled

Issue - State: closed - Opened by benalric over 3 years ago - 3 comments

#1367 - Error in filterAndTrim

Issue - State: closed - Opened by rwiscor over 3 years ago - 2 comments

#1364 - Nanopore variable region sequencing analysis

Issue - State: open - Opened by CarlaCristinaUranga over 3 years ago - 8 comments
Labels: question

#1363 - Abundance of dereplicated and denoised reads doesn't match

Issue - State: closed - Opened by MegaRamakodi over 3 years ago - 3 comments

#1362 - Error Message

Issue - State: closed - Opened by markdjohnson over 3 years ago - 5 comments

#1361 - Reproducing DADA2 output of the Extreme data set

Issue - State: closed - Opened by NicolasNaepflin over 3 years ago - 1 comment

#1358 - Problem with using metadata

Issue - State: closed - Opened by Tinh1425 over 3 years ago - 2 comments

#1355 - DADA2 with Loop Genomics 16S long read data

Issue - State: closed - Opened by sgreimanbio over 3 years ago - 3 comments

#1354 - Error: node stack overflow

Issue - State: closed - Opened by gkpillay over 3 years ago - 7 comments

#1353 - chimera removal

Issue - State: closed - Opened by ARBramucci over 3 years ago - 1 comment

#1352 - plotQualityProfile incompatibleTypes message

Issue - State: closed - Opened by katmuell over 3 years ago - 3 comments

#1350 - Strange pattern of the seqtab

Issue - State: closed - Opened by xunwenchen over 3 years ago - 10 comments

#1349 - error in filterAndTrim: subscript is out of bounds

Issue - State: closed - Opened by karaandres over 3 years ago

#1348 - recommended software/parameters for tree reconstruction

Issue - State: closed - Opened by csmiguel over 3 years ago - 5 comments

#1345 - removeBimeraDenovo command in dada2 (chimera removal step)

Issue - State: closed - Opened by DhebbieF over 3 years ago - 2 comments

#1343 - Error model fit

Issue - State: closed - Opened by Andreas-Bio over 3 years ago - 8 comments

#1341 - Filterandtrim error "IncompatibleTypes"

Issue - State: closed - Opened by jessicatittl over 3 years ago - 7 comments

#1340 - error when using filterAndTrim

Issue - State: closed - Opened by lauraewing over 3 years ago - 7 comments

#1339 - assign feature ids?

Issue - State: closed - Opened by afgovindarajan over 3 years ago - 1 comment

#1337 - importing dada2_sequencetable file to R

Issue - State: closed - Opened by riojatikusuma30 over 3 years ago - 1 comment

#1335 - Escherichia/Shigella species in assignSpecies results

Issue - State: closed - Opened by mammerlin over 3 years ago - 3 comments

#1332 - How to cope with significant differences in sequencing depth?

Issue - State: closed - Opened by vfonti over 3 years ago - 11 comments

#1328 - PacBio 16s rRNA full length sequence analysis

Issue - State: closed - Opened by sramani-spark over 3 years ago - 8 comments

#1320 - Primer removal with dada2/cutadapt in R

Issue - State: closed - Opened by tgaire over 3 years ago - 5 comments

#1315 - Does assigntaxonomy remove some reference sequences from customized DB?

Issue - State: closed - Opened by mammerlin over 3 years ago - 4 comments

#1312 - dada2 (Silva_metaxa2 training set) -Interesting expanded training set

Issue - State: closed - Opened by anrongloh93 over 3 years ago - 7 comments

#1307 - Binned quality scores and their effect on (non-decreasing) trans rates

Issue - State: open - Opened by JacobRPrice over 3 years ago - 63 comments
Labels: enhancement, question

#1306 - Error for filterAndTrim

Issue - State: closed - Opened by padpadpadpad over 3 years ago - 1 comment
Labels: bug

#1305 - Unexplained batch effect

Issue - State: closed - Opened by Fedorov113 over 3 years ago - 2 comments

#1301 - addSpecies for ITS data

Issue - State: open - Opened by aliruizrodriguez over 3 years ago - 9 comments
Labels: documentation

#1297 - Usage of parallelism to improve performance

Issue - State: closed - Opened by caio-davi over 3 years ago - 1 comment

#1293 - Silva missing ranks incorrectly propagated into DADA2-formatted database by `dada2:::makeTaxonomyFasta_SilvaNR()`

Issue - State: open - Opened by mikemc over 3 years ago - 22 comments
Labels: documentation

#1281 - BigDataPaired - Error in loop sequence

Issue - State: open - Opened by clairewoodall over 3 years ago - 3 comments
Labels: documentation, Priority

#1186 - Update GTDB hyperlink in tutorial pages

Issue - State: open - Opened by dadahan about 4 years ago - 4 comments
Labels: documentation, Priority

#1178 - Can't specify a length 2 vector for `compress=` in filterAndTrim()

Issue - State: closed - Opened by cpauvert about 4 years ago - 2 comments
Labels: documentation

#1149 - "random_device: rdseed failed" error in assignTaxonomy()

Issue - State: closed - Opened by vrbacky about 4 years ago - 2 comments
Labels: bug

#1124 - Escherichia/Shigella species level classificaiton missing with version 2 of the SILVA release

Issue - State: closed - Opened by nr0cinu about 4 years ago - 4 comments
Labels: bug

#1115 - Fully reproducible assignTaxonomy with random number initialization

Issue - State: open - Opened by max-mose-diversigen about 4 years ago - 12 comments
Labels: enhancement

#1086 - pooling TRUE vs. pseudo-pool, ASV disappearing

Issue - State: closed - Opened by Andreas-Bio over 4 years ago - 5 comments

#1035 - A lot of reads lost (>50%) after chimera check

Issue - State: closed - Opened by shyam-mayengbam over 4 years ago - 6 comments

#1028 - Assign Taxonomy UNITE8.2 error

Issue - State: closed - Opened by enurta2020 over 4 years ago - 8 comments
Labels: bug

#990 - Best practice for PacBio taxonomic assignment?

Issue - State: open - Opened by cjfields over 4 years ago - 9 comments
Labels: enhancement, question

#989 - removePrimers misses valid primer matches in certain circumstances

Issue - State: open - Opened by gmagoon over 4 years ago - 5 comments
Labels: question

#986 - learnErrors() very time consuming

Issue - State: closed - Opened by hias90 over 4 years ago - 6 comments

#974 - removeBimeraDenovo crashes after a long running time!

Issue - State: closed - Opened by Ellie-BM over 4 years ago - 19 comments

#947 - Clustering ASVs after DADA2? generating new OTU table

Issue - State: closed - Opened by lplough almost 5 years ago - 36 comments

#946 - Allow any header format of the reference taxonomy

Issue - State: closed - Opened by wbazant almost 5 years ago - 2 comments

#935 - segfaults due to zero-length reads in input

Issue - State: open - Opened by Puumanamana almost 5 years ago - 11 comments
Labels: bug

#902 - Update Big Data workflow in light of recent package improvements

Issue - State: open - Opened by benjjneb almost 5 years ago - 1 comment
Labels: tutorial

#872 - Propagate file paths to the output of derepFastq and dada

Issue - State: open - Opened by benjjneb about 5 years ago - 2 comments
Labels: enhancement, Priority

#866 - Non-corresponding derep-class and dada-class objects.

Issue - State: closed - Opened by thecrobe about 5 years ago - 8 comments

#821 - Possible issue with Illumina two color over-confidence in G

Issue - State: closed - Opened by michael-weinstein over 5 years ago - 4 comments
Labels: help wanted

#816 - sample inference error: object qmax not found when USE_QUALS=FALSE

Issue - State: closed - Opened by nextgenusfs over 5 years ago - 5 comments
Labels: bug

#798 - Maximum sequence length error

Issue - State: closed - Opened by aldendirks over 5 years ago - 7 comments
Labels: enhancement

#797 - Removing chloroplast ASVs & discrepancy between assignTaxonomy & IdTaxa

Issue - State: closed - Opened by pdcountway over 5 years ago - 11 comments
Labels: tutorial

#791 - Consequences of using dada2 on NovaSeq data

Issue - State: open - Opened by hhollandmoritz over 5 years ago - 48 comments
Labels: enhancement, Priority

#785 - Discuss `--discard-untrimmed` cutadapt flag in ITS tutorial?

Issue - State: open - Opened by roey-angel over 5 years ago - 4 comments
Labels: tutorial

#772 - Merge pairs number of mismatches

Issue - State: closed - Opened by sgavril over 5 years ago - 9 comments

#759 - Nanopore consensus sequencing and DADA2

Issue - State: closed - Opened by alexpiper over 5 years ago - 15 comments

#749 - Better integrate the pool and pseudo pages

Issue - State: open - Opened by benjjneb over 5 years ago
Labels: documentation

#729 - Lambda out-of-range error

Issue - State: closed - Opened by rebbec over 5 years ago - 9 comments
Labels: bug

#716 - Combining dada2 runs

Issue - State: closed - Opened by claireonthecouch over 5 years ago - 28 comments

#702 - Which UNITE data set to chose

Issue - State: closed - Opened by bernt-matthias over 5 years ago - 7 comments

#626 - Faster collapseNoMismatch()

Issue - State: open - Opened by masumistadler almost 6 years ago - 29 comments
Labels: enhancement

#618 - filterAndTrim: No reads passed the filter

Issue - State: closed - Opened by sfeds almost 6 years ago - 12 comments

#575 - Pipeline consensus sequence accuracy and Phred scores

Issue - State: closed - Opened by daov94 about 6 years ago - 2 comments

#565 - Concatenate improvement suggestion

Issue - State: closed - Opened by jgrzadziel about 6 years ago - 8 comments
Labels: enhancement

#553 - Coin toss ASV inference

Issue - State: open - Opened by AMCMC about 6 years ago - 3 comments
Labels: enhancement

#537 - merge and concatenation

Issue - State: closed - Opened by shyamrallapalli over 6 years ago - 3 comments

#496 - Allow extended prior sequences (e.g. full-length 16S)

Issue - State: open - Opened by AlexandreThibodeauUdM over 6 years ago - 3 comments
Labels: enhancement