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121,974 results • Page
234 of 2440
Sort: Rank
Rank
Views
Votes
Replies
2
votes
2
replies
915
views
Clustered bacterial RefSeq?
refseq
clustering
ANI
bacteria
2.2 years ago by
predeus
★ 2.1k
5
votes
10
replies
3.3k
views
7 follow
I want to rename sequence headers
Fasta
updated 2.2 years ago by
Hugo
▴ 400 • written 2.2 years ago by
Riyad
• 0
0
votes
1
reply
824
views
make error while installing MEGAcmd
megacmd
Ubuntu
MEGA
updated 2.2 years ago by
Jesse
▴ 880 • written 2.2 years ago by
shivankparashar
• 0
0
votes
0
replies
783
views
Passing parameters to gyppy_duplex pipeline
base-calling
ont
oxford-nanopore
guppy
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
Parham
★ 1.6k
0
votes
5
replies
1.4k
views
whole genome sequencing and assembly
assembly
whole-genome
sequencer
MGI
2.2 years ago by
manaswiniparija3
▴ 60
0
votes
5
replies
1.5k
views
Deepvariant and input CRAM files
Deepvariant
CRAM
updated 2.1 years ago by
GenoMax
154k • written 2.2 years ago by
biology.may20
▴ 20
5
votes
4
replies
1.7k
views
Find groups of SNP in a multi sample VCF with bcftools
vcf
SNP
bcftools
24 months ago by
Axzd
▴ 80
5
votes
5
replies
2.3k
views
bedtools coverage, Use “stdin”
Chip-seq
bedtools
updated 2.2 years ago by
Trivas
★ 1.9k • written 3.7 years ago by
Morris_Chair
▴ 370
0
votes
4
replies
1.1k
views
How to work with exome data
Exome
updated 2.2 years ago by
GenoMax
154k • written 2.2 years ago by
Lucía
• 0
1
vote
1
reply
964
views
How to solve, Error, the column headings: are not unique. in Build Transcript and Gene Expression Matrices
trinityrnaseq
rna-seq
updated 2.2 years ago by
Asaf
10k • written 2.2 years ago by
mavs_007
• 0
0
votes
0
replies
534
views
Gene Synteny
Synteny
conservation
gene
2.2 years ago by
prs
▴ 20
0
votes
4
replies
1.3k
views
Batch Effect Removal on non-Linearly independent samples
batch
rna-seq
ngs
updated 2.2 years ago by
Asaf
10k • written 2.2 years ago by
James
• 0
1
vote
2
replies
1.1k
views
whole genome
methylation
updated 2.2 years ago by
GenoMax
154k • written 2.2 years ago by
ali
• 0
1
vote
1
reply
1.1k
views
Phylogenetic analysis through sliding windows in VCF
phylogenetic-tree
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
hollymolly
▴ 10
0
votes
1
reply
1.4k
views
Identify binding motifs within large super enhancer region
MEME
Jaspar
enhancer
Homer
motifs
super
updated 2.2 years ago by
Alex Reynolds
36k • written 2.2 years ago by
mkunika
• 0
95
votes
23
replies
122k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 20 months ago by
clara.apicella
• 0 • written 7.2 years ago by
otwtgin2010
▴ 630
7
votes
2
replies
1.5k
views
How to transform rownames of a RNA Seq dataset with gene names to ENSG format?
GeneID
RNA-seq
Ensembl
GSEA
updated 2.2 years ago by
Radu Tanasa
▴ 150 • written 2.2 years ago by
Manuel Sokolov Ravasqueira
▴ 110
0
votes
2
replies
859
views
scRNAseq: integration downstream analysis and identification genes altered in one condition
scRNAseq
R
integration
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
camillab.
▴ 160
0
votes
2
replies
1.9k
views
FindAllMarkers in Seurat and statistical problem
statistical-testing
seurat
FindAllMarkers
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
piotto
▴ 20
1
vote
1
reply
685
views
Combine multiple fastq.gz files
linux
fastq
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
Zitian
• 0
10
votes
9
replies
6.2k
views
Remove sequences with (50% gaps) from MSA
Multiple-Sequence-Alignment
sequence
MSA
alignment
updated 2.2 years ago by
Mensur Dlakic
★ 30k • written 5.5 years ago by
nataliagru1
▴ 90
0
votes
0
replies
649
views
Haplotype network/phylogeny of 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 22 months ago by
Ram
45k • written 2.2 years ago by
Morgan
• 0
0
votes
2
replies
1.1k
views
Sample size estimation with ssizeRNA in R
transcriptomics
power-analysis
RNA-seq
sample-size-estimation
2.1 years ago by
Nana
• 0
1
vote
1
reply
1.2k
views
TXT or IDAT format for differential DNA Methylation analysis
NGS
updated 2.2 years ago by
Hamid Ghaedi
3.3k • written 2.2 years ago by
ananta.kapoor
• 0
2
votes
2
replies
1.1k
views
Download rRNAs.fasta for all bacteria from database
wget
NCBI
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
kamanovae
▴ 100
0
votes
0
replies
1.1k
views
ciTools error with lme4 and add_ci: Error in quantile.default(newX[, i], ...) : missing values and NaN's not allowed if 'na.rm' is FALSE
GLMMs
troubleshooting
R
ciTools
lme4
2.2 years ago by
Corey
• 0
2
votes
0
replies
862
views
News:
Registration open for Nextflow Summit 2023, and free online Nextflow / nf-core training
nextflow
2.2 years ago by
Marcel Ribeiro-Dantas
▴ 610
0
votes
0
replies
596
views
Converting RNA-seq expression profile into Coexpression
coexpression-network
RNA-seq
gene-expression
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
Mehvi khan
• 0
1
vote
2
replies
978
views
genotype frequency API/download
R
gnomad
python
api
2.2 years ago by
Barista
▴ 10
10
votes
6
replies
2.7k
views
adding features to gtf file using agat tool function
gtf
updated 2.2 years ago by
Juke34
9.3k • written 2.2 years ago by
1769mkc
★ 1.3k
4
votes
11
replies
2.6k
views
Gene Set Comparison Without Expression Data
gene-set-enrichment-analysis
R
updated 2.2 years ago by
Papyrus
★ 3.1k • written 2.2 years ago by
Eliza
▴ 30
6
votes
2
replies
1.5k
views
scRNAseq error source a custom function
R
scRNA-seq
updated 2.2 years ago by
Hamid Ghaedi
3.3k • written 2.2 years ago by
camillab.
▴ 160
0
votes
2
replies
830
views
TRIMMOMATIC ERROR ON WINDOWS/CYGWIN
windows
cygwin
trimmomatic
updated 2.2 years ago by
GenoMax
154k • written 2.2 years ago by
Beyza
• 0
2
votes
3
replies
1.4k
views
Getting hg38 chromosome positions of hg19 variants
hg38
variant-annotation
hg19
annovar
2.2 years ago by
Can Abdullah
• 0
0
votes
5
replies
1.4k
views
strelka variant calling
variant-calling
strelka
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
fra.r.silvestro
▴ 10
1
vote
3
replies
777
views
genome a specific country
genome
NCBI
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
m.esmaeilpour
▴ 10
0
votes
2
replies
1.3k
views
Lollipop plots for structural variation coordinates
vcf
sv
bioconductor
structural-variation
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
Dimitri
• 0
1
vote
2
replies
1.1k
views
BWA MEM -K option
alignment
bwa
updated 2.2 years ago by
DBScan
▴ 530 • written 2.2 years ago by
Yihang
• 0
0
votes
2
replies
1.9k
views
BLAST Tools: asn2gb????
asn2gb
BLAST-Tools
updated 2.2 years ago by
h.collage
• 0 • written 9.9 years ago by
ab.tsubaki
▴ 50
1
vote
10
replies
3.9k
views
Deepvariant variant calling by singularity
deepvariant
singularity
conda
docker
updated 2.0 years ago by
jeffhsu3
• 0 • written 2.3 years ago by
fra.r.silvestro
▴ 10
2
votes
2
replies
1.0k
views
Are SAM attributes necessary if I only keep the BAM files using STAR?
BAM
SAM
RNA-seq
STAR
updated 2.2 years ago by
GenoMax
154k • written 2.2 years ago by
ev97
▴ 40
2
votes
5
replies
1.4k
views
How to create a series of descending string in a column in data frame in R
R
updated 2.2 years ago by
Basti
★ 2.1k • written 2.2 years ago by
Mohamed Samir
▴ 30
0
votes
0
replies
819
views
MaxQuant - second peptide search
peptide-search
proteome
maxquant
updated 2.2 years ago by
Ram
45k • written 2.2 years ago by
anu014
▴ 190
6
votes
5
replies
2.2k
views
How can there be numerous high quality heterozygous y chromosome alleles not within pseudoautosomal regions across chrY in WGS data?
heterozygous-y
updated 2.2 years ago by
LauferVA
4.8k • written 2.3 years ago by
Charles R.
▴ 10
1
vote
0
replies
652
views
Looking to expand annotation of kegg in data frame R
kegg
orthologs
annotations
R
updated 2.2 years ago by
zx8754
12k • written 2.2 years ago by
microecologist93
▴ 20
0
votes
1
reply
801
views
FINDFUNGI Pipeline
metagenomics
findfungi
kraken
updated 2.2 years ago by
dthorbur
★ 3.1k • written 2.2 years ago by
houssi301
• 0
7
votes
7
replies
2.3k
views
Help speeding up C++ algorithm to assign elemental composition to single m/z (=mass) value
Cpp
Rcpp
spectrometry
mass
2.2 years ago by
bkleiboeker
▴ 370
1
vote
6
replies
1.6k
views
issue regarding download SRA file in bulk
sra-toolkit
ncbi-sra
coding
2.2 years ago by
microorganism_001
▴ 30
1
vote
2
replies
4.0k
views
Tool:
How Study Aromatic-Aromatic Interactions And Amino-Aromatic Interactions Of Protein-Ligands Complexes In The Pdb.
pdb
updated 2.2 years ago by
Jiyao Wang
▴ 380 • written 11.9 years ago by
bagaruwa
• 0
6
votes
3
replies
5.1k
views
Generate Image Of Pdb File From Script Or Command Line
pdb
updated 2.2 years ago by
Jiyao Wang
▴ 380 • written 13.8 years ago by
NPalopoli
▴ 290
121,974 results • Page
234 of 2440
Recent Votes
Comment: how to respond that my research does not have experimental validation
Comment: how to respond that my research does not have experimental validation
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Answer: infercnv error at STEP 18 - file descriptor is too large for select()
A: bwa for multiple fastq files
A: bwa for multiple fastq files
Comment: Issue about generating EMBL Flat file for ENA submission
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Answer: how to respond that my research does not have experimental validation
by
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★ 30k
People publish predictive papers all the time that have zero experimental support. There are different degrees of "lacking experimental val…
Comment: how to respond that my research does not have experimental validation
by
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89k
You should give the reviewer something. An independent way of in silico validation, other supporting analysis. Just "no" might lead to reje…
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▴ 40
I believe ONT recommends Minimap2. This is also the default tools in their EPI2ME workflow.
Comment: how to respond that my research does not have experimental validation
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Yes, and if you are going to mention that experimental validation is not possible or outside the scope of your paper, kindly remind the rev…
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154k
Is it possible that mismatched R1/R2 files were used in one of the steps? If you are sure that has not happened then you could try to see…
Comment: Quantification using salmon in alignment-based mode after minimap2 run
by
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154k
In case you were not aware ONT also provides a transcriptome workflow for long reads: https://github.com/epi2me-labs/wf-transcriptomes
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by
ATpoint
89k
Either do experimental validation, or say that not possible due to lack of collaboration, infrastructure, lab background. If they reject, s…
Answer: Quantification using salmon in alignment-based mode after minimap2 run
by
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7.1k
As @atpoint suggests, you must align against the transcriptome. Also, the other relevant flags should be set (i.e. `--secondary=no` will di…
Answer: Quantification using salmon in alignment-based mode after minimap2 run
by
ATpoint
89k
Yes, must strictly be transcriptome. Reference from developer: https://www.biostars.org/p/9556364/
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
Yes, they removed the adapters, so I did not have to do extra steps for this (other than Trimmomatic within Trinity to get rid of short con…
Answer: infercnv error at STEP 18 - file descriptor is too large for select()
by
yura.grabovska
▴ 830
Noticed that running `infercnv::CreateInfercnvObject()` generates a warning: ``` WARN [2025-10-06 14:43:38] Please use "options(scipen = …
Comment: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
by
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Thank you for your reply. I’m currently trying to perform alignments using both aligners, but I wanted to ask if anyone has conducted a si…
Comment: Which aligner is more suitable for ONT R10.4.1 Dorado-corrected reads: minimap2
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8.0k
Good summary. I never tried winnowmap despite it's apparent advantages. If you have really repeat rich regions like centromeres that it may…
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154k
Please post direct links to software you mention. Not sure why you are using LinkedIn short URL's. Historically downloads from JGI have be…
Comment: Hifiasm is getting killed while trying to assemble a genome
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pranavdatar01
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This is the paper: https://doi.org/10.3389/fevo.2022.850817 (Genome of Varanus salvator macromaculatus (Asian Water Monitor) Reveals Adapta…
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