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13,509 results • Page
2 of 271
Sort: Rank
Rank
Views
Votes
Replies
4
votes
2
replies
297
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 1 day ago by
Juke34
8.5k • written 1 day ago by
njornet
▴ 20
1
vote
0
replies
153
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
1 day ago by
Novogene
▴ 420
0
votes
1
reply
393
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 1 day ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
3
votes
3
replies
460
views
Korean human genome reference file
GWAS
reference
imputation
1 day ago by
SeoGyun
• 0
3
votes
4
replies
418
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 1 day ago by
GenoMax
141k • written 2 days ago by
n_navy
• 0
0
votes
0
replies
146
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 1 day ago by
Ram
43k • written 2 days ago by
bioinfo223
▴ 10
0
votes
0
replies
159
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
2 days ago by
P.
• 0
0
votes
0
replies
150
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
2 days ago by
ekirsch
• 0
1
vote
1
reply
338
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
16 hours ago by
renan.igor
• 0
1
vote
1
reply
227
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 2 days ago by
Ram
43k • written 2 days ago by
anasjamshed
▴ 120
3
votes
1
reply
582
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 2 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
0
votes
0
replies
151
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
2 days ago by
synat.keam
▴ 100
0
votes
1
reply
240
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 2 days ago by
GenoMax
141k • written 2 days ago by
ycts
• 0
5
votes
4
replies
579
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq
EdgeR
DEGs
DESeq2
1 day ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
253
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf
bam
bcf
snps
updated 2 days ago by
LChart
3.9k • written 2 days ago by
George
▴ 10
0
votes
4
replies
535
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
1 day ago by
Kai Xin
• 0
1
vote
1
reply
207
views
Retrieve a % coverage for each transcript
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
jammydodger123456
▴ 40
0
votes
1
reply
323
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 2 days ago by
Klaus S
▴ 150 • written 8 days ago by
Zeng Hao
▴ 40
0
votes
2
replies
331
views
How can I solve this error?
metal
2 days ago by
22211020193
• 0
0
votes
0
replies
156
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 2 days ago by
GenoMax
141k • written 2 days ago by
srimmer
• 0
1
vote
2
replies
243
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 2 days ago by
Ram
43k • written 2 days ago by
aniigodwinn
• 0
2
votes
3
replies
380
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
1 day ago by
valentinatsar
• 0
2
votes
3
replies
262
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 2 days ago by
Michael
54k • written 2 days ago by
LDT
▴ 330
2
votes
10
replies
639
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 1 day ago by
GenoMax
141k • written 2 days ago by
me
• 0
2
votes
2
replies
355
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
1 day ago by
nhaus
▴ 300
0
votes
0
replies
308
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
2 days ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 2 days ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
7
replies
737
views
Removing duplicates
duplicates
ONT
minimap2
updated 1 day ago by
joe
▴ 510 • written 2 days ago by
quentinperriere
• 0
0
votes
1
reply
172
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 2 days ago by
DKA
▴ 40 • written 2 days ago by
james.melhorn
• 0
3
votes
4
replies
376
views
biomaRt error for different R version
biomaRt
R
updated 1 day ago by
GenoMax
141k • written 2 days ago by
manaswwm
▴ 490
0
votes
1
reply
162
views
Freyja plot error
Freyja
updated 2 days ago by
Ram
43k • written 2 days ago by
Adyasha
• 0
1
vote
2
replies
172
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
3 days ago by
hagl
▴ 10
0
votes
0
replies
142
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
3 days ago by
chemokine-1
▴ 10
0
votes
4
replies
447
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
2 days ago by
feather-W
• 0
0
votes
0
replies
207
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 2 days ago by
Michael
54k • written 3 days ago by
jonrkarr
▴ 100
0
votes
2
replies
188
views
Bedmethyl file format
bedmethyl
methylation
updated 2 days ago by
GenoMax
141k • written 3 days ago by
njornet
▴ 20
0
votes
0
replies
155
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
3 days ago by
Ali
• 0
2
votes
4
replies
283
views
SnpEff annotates coding duplication as intronic?
snpeff
3 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
218
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
2 days ago by
mropri
▴ 150
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 3 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
581
views
Piping samtools to R
R
NGS
bash
samtools
3 days ago by
joe
▴ 510
2
votes
2
replies
214
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 3 days ago by
bk11
★ 2.3k • written 3 days ago by
bgbs
• 0
3
votes
7
replies
397
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
3 days ago by
ntsopoul
▴ 60
0
votes
0
replies
132
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
3 days ago by
shasabhi1
• 0
0
votes
0
replies
125
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
3 days ago by
Nishat
• 0
3
votes
3
replies
385
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
3 days ago by
ayushm64
• 0
0
votes
0
replies
137
views
what exactly is a k-mer table (remora)?
remora
basecall
3 days ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 3 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
355
views
Rename multiple fastq.gz files
fastq
next-gen
updated 3 days ago by
shenwei356
8.4k • written 3 days ago by
Jérémie
• 0
1
vote
1
reply
159
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 3 days ago by
dsull
★ 5.8k • written 3 days ago by
niruf
• 0
13,509 results • Page
2 of 271
Recent Votes
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Ciriquant not configuring hisat2 indexed files
bcftools multiple commands
bcftools pipe generated file from first command with second
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Scholar
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★ 2.4k
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Rodolfo Adrián
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▴ 70
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Recent Replies
Comment: Free/open source 23andme-like analysis
by
swbarnes2
14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
swbarnes2
14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
ATpoint
81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
by
swbarnes2
14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
Answer: MEGA Analysis Issue on High-Performance Computer
by
Mensur Dlakic
★ 27k
> I have ensured that I am using the latest version of MEGA and that other applications are not consuming excessive resources during the an…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Some of us are still learning and fall foul to knowledge limitation fairly regularly. Luckily we have people to put us in our place.
Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
by
GenoMax
141k
> I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. You c…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
rheab1230
▴ 140
I got the normalized gene count from gtex portal. they use inverse quantile normalization
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
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