benjjneb dada2 issues - Githubissues

benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution

http://benjjneb.github.io/dada2/

GNU Lesser General Public License v3.0

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issues

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Pooling, big data and classic tutorial

#1977 luigallucci closed 1 day ago
3
Is there any way to further speed up dada?

#1976 constructivedio opened 1 day ago
3
When processing full-length 16S data, the ASV table output by makeSequenceTable has an unusually low number of sequences in the sample

#1975 M-o-Y-u opened 1 week ago
11
Using screen background to remove noise with dada2 times error.

#1974 GoldLIU opened 1 week ago
4
Assigning sample names, time points, etc. in phyloseq step

#1973 backwards-charm opened 1 week ago
3
The deprecated feature was likely used in the dada2 package.

#1972 sar515 closed 2 weeks ago
1
Problem with taxa assignation

#1971 martina-nasuelli opened 2 weeks ago
3
Keeping missing data / Ns in the reads

#1970 ThomePauline closed 2 weeks ago
1
ONT error model [question]

#1969 ccrinconc closed 2 weeks ago
2
Merging two V4 runs together

#1968 MadsBjornsen opened 3 weeks ago
0
None of my Lactobacillus genus have been assigned species after using assignTaxonomy. Please assist

#1967 asavelaolona closed 2 weeks ago
2
Cluster to OTU, not ASVs?

#1966 mya-darsan opened 3 weeks ago
3
error laoding the dada2 library

#1965 marwa38 opened 4 weeks ago
5
Add tracking and checking or guidance on what chimera removal method to use based on dada pooling mode

#1964 benjjneb opened 1 month ago
0
DADA2 Error Rate Plots

#1963 goodguynickpt closed 3 weeks ago
16
Expand tutorial callouts for other sequencing technologies

#1962 benjjneb opened 1 month ago
0
`plotErrors` improvements: Drop zero-observation points and scale points by number of observations

#1961 benjjneb opened 1 month ago
2
Update deprecated tutorials to make their deprecation clear

#1960 benjjneb opened 1 month ago
1
Segmentation fault core dumped on the derep step with Kinnex full length reads

#1959 sbedwell27 closed 1 month ago
6
Is it possible to get ASVs with zero counts in all samples after DADA2 run?

#1958 Anto007 closed 1 month ago
4
High chimera rate: +80%

#1957 Mx-nene closed 1 month ago
4
R session gets aborted during dereplication of reverse reads

#1956 Reeshma01 closed 1 month ago
1
Unexpected results after cutadapt

#1955 jesika0123 closed 1 month ago
4
derep

#1954 tobaiasbama closed 1 month ago
1
Trimming/ derep error

#1953 tobaiasbama closed 1 month ago
3
Is denoising required for kraken analysis?

#1952 BrinthaVP closed 1 month ago
4
Suspiciously high number of low-abundance ASVs (10s of 1000s)?

#1951 SJohnsonMayo closed 1 month ago
2
Cluster ASVs to OTUs with DECIPHER

#1950 Danyang1111 closed 1 month ago
3
cutadapt: error: cutadapt not able to trim the desired adaptor

#1949 faizee-ali closed 1 month ago
2
quality filter: imbalance forward vs reverse reads - dada2-

#1948 valengirardi closed 1 month ago
3
Increasing number of nonchimeric reads compared to the number of input reads

#1947 Abdelrahim-maker opened 1 month ago
8
Solving the "Error: BiocParallel errors" (in almost every sample)

#1946 Yoonseopark02 closed 1 month ago
5
Solving the "Error: BiocParallel errors", in almost every sample analysis

#1945 Yoonseopark02 closed 1 month ago
0
Clustering dada2-obtained ASVs into OTUs with DECIPHER

#1944 ConstanceBtd closed 1 month ago
7
dada2 reference database for eukaryotes

#1943 eunicetan closed 1 month ago
1
Differences in chimera detection based on dataset structure

#1942 seoldh opened 1 month ago
2
error: no input files found from Assign taxonomy

#1941 bylee613 closed 1 month ago
5
BiocParallel error

#1940 ThibauldMichel closed 1 month ago
5
Number of ASVs changes on different computers/R versions?

#1939 vmsur closed 1 month ago
4
Taxonomy assignment

#1938 SRC151 closed 1 month ago
4
Non-fitting Error Plots

#1937 SophMN closed 1 month ago
4
Quality plot profile refence for filterAndTrim truncLen values

#1936 luigallucci closed 1 month ago
5
Drop in Qualityscore in the middle of the reads

#1935 MadsBjornsen closed 1 month ago
8
Don't know if singletons are being removed or not

#1934 migfejo closed 2 months ago
2
Missing reads when transitioning from Dada2 to phyloseq

#1933 GingerMATE closed 1 month ago
3
Memory error in AssignTaxonomy when working with very small sequences

#1932 nearinj opened 2 months ago
1
AIUTO file parsing

#1931 chiaragiovannetti11111 closed 2 months ago
1
garbled fastq files after Filter and trim

#1930 Danyang1111 closed 1 month ago
1
Problem trimming primers

#1929 Gian77 closed 1 month ago
2
Loosing reads after merging

#1928 hellewiedunkle closed 1 month ago
5