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6
votes
7
replies
1.1k
views
Genes looking differential abundant are not accoring to DESeq2
Deseq2 R
updated 2.0 years ago by 100k • written 2.0 years ago by ▴ 80
6
votes
10
replies
15k
views
6 follow
Deseq error : ncol(countData) == nrow(colData) is not TRUE
genome
written 4.3 years ago by ▴ 80
1
vote
1
reply
515
views
Circos.heatmap not displaying zero values in R
visualisation R
2.2 years ago by robert.murphy ▴ 80
0
votes
2
replies
833
views
DESeq2 on metagenomic gene abundance data, should I normalize for total sample depth?
Deseq2 metagenome R
2.3 years ago by robert.murphy ▴ 80
0
votes
0
replies
447
views
EnhancedVolcano selectLab() for custom labels but only those above Pvalue threshold
EnhancedVolcano Deseq2 R
2.3 years ago by robert.murphy ▴ 80
5
votes
3
replies
1.2k
views
Can an enzyme have multiple EC numbers?
hotpep expasy enzyme
updated 2.4 years ago by 15k • written 2.4 years ago by ▴ 80
0
votes
6
replies
1.3k
views
What is the best tool to recover nitrogen cycling genes from an annotated assembly?
annotation
2.4 years ago by robert.murphy ▴ 80
0
votes
0
replies
431
views
How to calculate mapping rate per contig of an assembly scaled by contig length?
assembly alignment metagenome
2.4 years ago by robert.murphy ▴ 80
0
votes
0
replies
519
views
How to reintroduce sample divisions to a metagenomic co-assembly, what are the best practices?
coverage assembly metagenomic
2.4 years ago by robert.murphy ▴ 80
0
votes
0
replies
498
views
Is there any reason to discard singletons after de-hosting metagenomic reads?
alignment metagenome
2.5 years ago by robert.murphy ▴ 80
0
votes
2
replies
919
views
paired reads have different names BWA MEM after samtools bam > fastq
alignment
2.6 years ago by robert.murphy ▴ 80
1
vote
4
replies
1.3k
views
How to get summary statistics out of bbduk.sh ?
quallity sequencing control
2.6 years ago by robert.murphy ▴ 80
5
votes
6
replies
1.6k
views
Should you normalization metagenomic data
metagenomic coverage assembly
2.6 years ago by robert.murphy ▴ 80
0
votes
0
replies
489
views
K-mer coverage of metgenomic data, what is the uper limit of K?
metagenomic coverage
2.6 years ago by robert.murphy ▴ 80
0
votes
8
replies
2.0k
views
Mapping contigs back to samples from co-assembled metagenome.
coassembly
2.6 years ago by robert.murphy ▴ 80
0
votes
3
replies
1.0k
views
Metagenomic assembly, removing redundant contigs.
metagenome assembly
updated 2.6 years ago by 11k • written 2.6 years ago by ▴ 80
0
votes
0
replies
459
views
What would the assortativity of a putative mirobial interaction network tell you in an evological setting?
graphs 16S network
2.6 years ago by robert.murphy ▴ 80
3
votes
5
replies
1.4k
views
Genome assembly, removal of conting below 300 bp?
assembly
updated 2.6 years ago by 15k • written 2.6 years ago by ▴ 80
4
votes
3
replies
4.3k
views
What is the correct syntax for BioPythons SeqIO.parse()
assembly biopython
updated 2.7 years ago by 8.5k • written 2.7 years ago by ▴ 80
1
vote
4
replies
779
views
How to get from annotated sequences to UniProt IDs
annotation
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by ▴ 80
0
votes
3
replies
819
views
Combining distance matricies between multiple aligned genes into final distance matrix
phylogeny distance alignment
3.0 years ago by robert.murphy ▴ 80
0
votes
1
reply
687
views
Estimating error rate across my 16S MiSeq amplicon sequencing
sequencing amplicon MiSeq error
updated 3.0 years ago by 3.6k • written 3.0 years ago by ▴ 80
0
votes
3
replies
975
views
How to interpret min-hash values in phylogeny
phylogeny mash alignment
updated 3.0 years ago by 35k • written 3.0 years ago by ▴ 80
0
votes
4
replies
945
views
Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect
bedtools annotation gtf
3.0 years ago by robert.murphy ▴ 80
8
votes
7
replies
1.5k
views
Whole genome species clustering
phylogeny assembly phylogenetics
updated 8 months ago by ▴ 10 • written 3.1 years ago by ▴ 80
0
votes
2
replies
687
views
16S Barcoding long and short sequences return different BLAST results
barcoding 16S
3.1 years ago by robert.murphy ▴ 80
2
votes
20
replies
4.8k
views
Converting Braker2 gtf output to gff then genbank
annotation
3.1 years ago by robert.murphy ▴ 80
2
votes
5
replies
1.4k
views
How to solve multiple CDS features with same locus tag in EMBL format
annotation embl
updated 3.1 years ago by 142k • written 3.1 years ago by ▴ 80
2
votes
4
replies
1.2k
views
GTF format feature definitions
annotation
updated 3.1 years ago by 19k • written 3.1 years ago by ▴ 80
0
votes
0
replies
419
views
Should one keep softmasking when combining gff+fasta to gbk format?
annotation
3.2 years ago by robert.murphy ▴ 80
0
votes
0
replies
341
views
Using Maker to map foward annotations from reference gff
annotation
3.2 years ago by robert.murphy ▴ 80
0
votes
9
replies
1.3k
views
BBMap not mapping reads to sequences known to exist in reference
alignment
updated 3.2 years ago by 142k • written 3.2 years ago by ▴ 80
0
votes
3
replies
609
views
Can you use high quallity annotation of very closely related to annotation novel genome
annotation
3.2 years ago by robert.murphy ▴ 80
0
votes
5
replies
1.1k
views
Mapping a short primer sequence to a whole genome
alignment
updated 3.2 years ago by 8.5k • written 3.2 years ago by ▴ 80
2
votes
4
replies
971
views
Does BBDUK remove "N" bases?
Assembly
updated 3.3 years ago by 142k • written 3.3 years ago by ▴ 80
0
votes
10
replies
1.4k
views
Blastn on illumina reads for contamination detection before or after quality filtering?
Assembly
updated 3.3 years ago by 20 • written 3.5 years ago by ▴ 80
4
votes
9
replies
960
views
Will coverage downsize of metagenomeic data drastically effect assembly?
Assembly
updated 3.4 years ago by ★ 27k • written 3.4 years ago by ▴ 80
0
votes
5
replies
1.7k
views
Do you NEED to bin a metagenome into MAGs?
Assembly binning
updated 3.4 years ago by 3.2k • written 3.4 years ago by ▴ 80
0
votes
0
replies
582
views
co-assembly bam file generation for metagenomic binning
Assembly binning
3.4 years ago by robert.murphy ▴ 80
2
votes
7
replies
789
views
To merge or not to merge during de novo assembly?
Assembly
3.5 years ago by robert.murphy ▴ 80
3
votes
7
replies
4.7k
views
BWA mem skip orientation RF/RR as there are not enough pairs
alignment
updated 3.5 years ago by 35k • written 3.5 years ago by ▴ 80
0
votes
4
replies
2.5k
views
How best to pick kmer's for spades assembly?
Assembly
3.5 years ago by robert.murphy ▴ 80
2
votes
4
replies
786
views
Samtools stats -F showing filtering from when and under what parameters?
alignment
3.5 years ago by robert.murphy ▴ 80
2
votes
7
replies
1.5k
views
Quallity trimming by phred score, how far is to far?
Assembly sequencing
updated 3.5 years ago by 142k • written 3.5 years ago by ▴ 80
0
votes
0
replies
600
views
Culture independent detection of bacterial biosynthetic gene clusters from microbiomes
genome metagenome BGC biosynthetic gene cluster
3.6 years ago by robert.murphy ▴ 80
1
vote
2
replies
1.2k
views
Normalization of raw Illumina reads.
sequencing Assembly
updated 3.6 years ago by 43k • written 3.6 years ago by ▴ 80
0
votes
5
replies
1.2k
views
Is it possible to supplement a gbk file with manual annotations?
annotation genome viral
updated 3.6 years ago by ★ 27k • written 3.6 years ago by ▴ 80
1
vote
13
replies
2.2k
views
SPAdes v3.14 unable to find files despite correct file path
Assembly
updated 2.9 years ago by ▴ 50 • written 3.6 years ago by ▴ 80
0
votes
0
replies
461
views
Are there methods to identify a bacteria as anaerobic or aerobic through its whole genome?
genome
updated 3.6 years ago by 20 • written 3.8 years ago by ▴ 80
0
votes
0
replies
697
views
Lastal aligner not detecting queery sequences
alignment
3.6 years ago by robert.murphy ▴ 80
63 results • Page 1 of 2
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