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0
votes
2
replies
668
views
should remove unassigned genera in 16S rRNA sequencing analysis
16S rRNA metagenomics sequencing
10 months ago by zhangdengwei ▴ 210
1
vote
0
replies
369
views
Alternative approach to rarefying in 16S rRNA analysis
16S Rarefying rRNA
11 months ago by zhangdengwei ▴ 210
0
votes
2
replies
816
views
too many zeros in 16S rRNA amplicon sequencing data
16S rRNA
11 months ago by zhangdengwei ▴ 210
0
votes
0
replies
356
views
Align shotgun metagenomics to reference protein database
reference protein metagenome database paladin
12 months ago by zhangdengwei ▴ 210
1
vote
2
replies
648
views
how to iteratively search sequences against sequence database using profile HMM
protein pHMM
14 months ago by zhangdengwei ▴ 210
1
vote
2
replies
713
views
how to evaluate a small increase in AUC
learning AUC machine
23 months ago by zhangdengwei ▴ 210
3
votes
4
replies
2.5k
views
a problem while using fastq-dump to split SRR files
software error
updated 2.4 years ago by ▴ 10 • written 5.1 years ago by ▴ 210
0
votes
0
replies
611
views
got error "need larger value of 'ncol' as pivoting occurred" when using adonis2
PERMANOVA adonis2
2.5 years ago by zhangdengwei ▴ 210
0
votes
2
replies
760
views
easy way to fetch out the surrounding CDS of a pair of given coordinates
GFF
2.7 years ago by zhangdengwei ▴ 210
0
votes
2
replies
712
views
fetch out common/conserved genes from a bunch of bacteria species
common analysis genes comparative
2.7 years ago by zhangdengwei ▴ 210
0
votes
0
replies
373
views
how to assign novel multilocus sequence type
microbioloy
3.0 years ago by zhangdengwei ▴ 210
0
votes
5
replies
1.9k
views
few genes were annotated to GO terms using online eggnog-mapper
GO KEGG eggnog-mapper
updated 3.2 years ago by 20 • written 3.3 years ago by ▴ 210
0
votes
1
reply
10k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA statistics metagenomics
updated 3.4 years ago by • 0 • written 4.4 years ago by ▴ 210
0
votes
0
replies
777
views
how to do the parametric trend analysis in R
trend analysis parametric R
3.5 years ago by zhangdengwei ▴ 210
0
votes
2
replies
1.0k
views
error when running Mauve to re-order contigs
comparative genome Mauve genome assembly
updated 3.6 years ago by • 0 • written 4.0 years ago by ▴ 210
0
votes
0
replies
855
views
how to select reference when constructing a SNP-based phylogenetic tree
phylogenetic tree SNP
3.6 years ago by zhangdengwei ▴ 210
0
votes
0
replies
740
views
predict plasmid from bacterial WGS
WGS bacteria plasmid chromosome
3.6 years ago by zhangdengwei ▴ 210
0
votes
1
reply
783
views
how to trust the taxa profile annotated by different softwares
metagenome taxa annotation metaphlan3 kraken2
3.7 years ago by zhangdengwei ▴ 210
0
votes
0
replies
1.4k
views
how to get the log file of pip in Conda
pip Conda
3.7 years ago by zhangdengwei ▴ 210
0
votes
4
replies
5.9k
views
how to get the installation history of conda
conda
3.7 years ago by zhangdengwei ▴ 210
3
votes
4
replies
1.3k
views
what's the best Kmer should be set when assembling bacteria genome
genome assembly Kmer
3.7 years ago by zhangdengwei ▴ 210
0
votes
0
replies
1.1k
views
how to obtain the abundance of superclass pathway of MetaCyc when using humann2 to do function analysis
humann2 MetaCyc pathway
3.7 years ago by zhangdengwei ▴ 210
0
votes
0
replies
564
views
compare the plamids of two bacteria
comparative genome plamids bateria
3.7 years ago by zhangdengwei ▴ 210
2
votes
6
replies
1.5k
views
how to annotate draft genome
contigs bacteria draft genome
updated 3.8 years ago by 3.6k • written 3.8 years ago by ▴ 210
3
votes
3
replies
1.9k
views
bootstraped spearman correlation in R
spearman correlation bootstraped spearmanRho
updated 3.8 years ago by 35k • written 3.8 years ago by ▴ 210
0
votes
2
replies
1.3k
views
Significantly different number of reads between two paired files when runing kneaddata
kneaddata metagenomics remove host reads
updated 3.9 years ago by 20 • written 4.0 years ago by ▴ 210
2
votes
4
replies
7.0k
views
meaning of CheckM output
genome assembly CheckM Contigs
updated 3.9 years ago by 10k • written 3.9 years ago by ▴ 210
5
votes
2
replies
1.8k
views
which better for the prediction of 16s rRNA
16s rRNA sequence prediction
updated 4.0 years ago by ★ 27k • written 4.0 years ago by ▴ 210
1
vote
5
replies
2.2k
views
what's meaning of parameter "-t rel_ab_w_read_stats"
metaphlan 3
4.0 years ago by zhangdengwei ▴ 210
3
votes
4
replies
2.1k
views
SAPdes not support single-end data?
metagenomics Assembly SAPdes
4.1 years ago by zhangdengwei ▴ 210
1
vote
3
replies
800
views
q-value > 1 in STAMP
statistics metagenomics STAMP q-value
4.1 years ago by zhangdengwei ▴ 210
0
votes
0
replies
1.2k
views
how to calculate Chao 1 with the input of relative abundance of microbiota
chao 1 metaphlan microbiota shannon
4.2 years ago by zhangdengwei ▴ 210
0
votes
1
reply
1.2k
views
adopt last KEGG database to do pathway enrichment in humman2
humann2 kegg
4.2 years ago by zhangdengwei ▴ 210
3
votes
11
replies
1.9k
views
how to merge two big file faster
shell cat
4.2 years ago by zhangdengwei ▴ 210
2
votes
2
replies
728
views
how to find the conserved region in two or more genomes
genome FASTA
updated 4.3 years ago by ▴ 330 • written 4.3 years ago by ▴ 210
0
votes
1
reply
1.1k
views
Unable to Visualize RGI results using JSON file upload
metagenomics CARD RGI
updated 4.4 years ago by 20 • written 4.5 years ago by ▴ 210
0
votes
3
replies
985
views
'HTSeq._HTSeq.GenomicInterval' object has no attribute 'xrange'
RNA-Seq python HTSeq
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 210
8
votes
5
replies
5.0k
views
DiffBind without replicates
ChIP-Seq R DiffBind
4.6 years ago by zhangdengwei ▴ 210
4
votes
3
replies
1.5k
views
Calculate p-value for experiment group with replicates, while control group without replicates
R RNA-Seq DESeq2 edgeR
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 210
0
votes
2
replies
1.5k
views
low mapping rate with bowtie2 and BWA, but not blast
RNA-Seq sequencing alignment
updated 5.0 years ago by 35k • written 5.0 years ago by ▴ 210
1
vote
8
replies
2.3k
views
how to compute the insert size in SAM file
alignment
updated 5.0 years ago by 20 • written 5.0 years ago by ▴ 210
1
vote
3
replies
2.1k
views
how to output the best alignment rather than multiple alignments for each read in BWA
alignment
updated 5.0 years ago by ★ 2.9k • written 5.0 years ago by ▴ 210
5
votes
17
replies
17k
views
7 follow
how to fix the error - Too many open files - by changing code in python3.7
software error
updated 14 months ago by • 0 • written 5.1 years ago by ▴ 210
8
votes
10
replies
2.2k
views
some unrelated info in SAM file generated by BWA
sequencing
updated 5.1 years ago by ▴ 100 • written 5.1 years ago by ▴ 210
1
vote
9
replies
2.3k
views
how to extract the gene sequence according to its coordinates on the reference genome?
sequence
5.1 years ago by zhangdengwei ▴ 210
0
votes
4
replies
765
views
how to get a read sequence from reference genome
sequence
5.1 years ago by zhangdengwei ▴ 210
2
votes
8
replies
1.6k
views
Approximate matching to find similar DNA sequence
genome
5.1 years ago by zhangdengwei ▴ 210
47 results • Page 1 of 1
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