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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
7
votes
14
replies
570
views
ggsave() bug in ggplot2?
R
ggplot2
updated 5 days ago by
Ram
39k • written 6 days ago by
Medeea
▴ 10
1
vote
7
replies
330
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
updated 4 days ago by
Ram
39k • written 5 days ago by
mohsamir2016
▴ 30
0
votes
8
replies
348
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 5 days ago by
GenoMax
129k • written 6 days ago by
Marta
• 0
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
2 days ago by
Maria17
▴ 20
3
votes
2
replies
212
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes
GRCh38
gnomad
assembly
freeze
updated 5 days ago by
Jeremy Leipzig
21k • written 6 days ago by
JourneyToAbyss
▴ 210
0
votes
1
reply
128
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat
single-cell
FindVariableFeatures
FindAllMarkers
RNA-Seq
updated 5 days ago by
rpolicastro
12k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
6
replies
375
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
2 days ago by
jrodrigu
• 0
1
vote
0
replies
97
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
6 days ago by
Jonathan Lefebre
▴ 70
8
votes
7
replies
391
views
including samples for which group is unknown to help adjust for another variable
TCGA
design
RNA-Seq
deseq2
updated 5 days ago by
Vincent Laufer
★ 2.9k • written 7 days ago by
pilargmarch
▴ 100
0
votes
2
replies
160
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER
DATABASE
PHP
1 day ago by
Souvik
• 0
4
votes
6
replies
316
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody
BD
updated 5 days ago by
Ram
39k • written 6 days ago by
abbas.waseem.gcu
▴ 20
0
votes
3
replies
180
views
DEGseq for multiple samples
DEGseq
DEG
updated 5 days ago by
Ram
39k • written 6 days ago by
ALOUSH ALI
• 0
4
votes
2
replies
178
views
How to calculate kinship matrix table from vcf file
variants
haplotyping
kinship
heatmap
updated 5 days ago by
chrchang523
10k • written 6 days ago by
rj.rezwan
• 0
1
vote
1
reply
121
views
How to convert bed file to vcf?
vcf
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
herh
• 0
0
votes
0
replies
80
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 5 days ago by
Ram
39k • written 6 days ago by
Rishabh Jha
• 0
1
vote
3
replies
210
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 5 days ago by
GenoMax
129k • written 6 days ago by
NikhilP
▴ 20
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 20 hours ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
1
reply
159
views
BAM creation - vg surject vs vg mpmap output
mpmap
surject
vg
bam
updated 6 days ago by
Rachel
• 0 • written 6 days ago by
AshleeThomson
• 0
0
votes
0
replies
106
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
6 days ago by
mbk0asis
▴ 670
0
votes
0
replies
303
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
199
views
Michigan Imputation Server - Local docker image
genotype
WGS
imputation
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 8 days ago by
batch_effect
• 0
0
votes
1
reply
165
views
Manhattan Plot with independent significant hits
Manhattan-plot
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 6 days ago by
en_keser
• 0
0
votes
0
replies
106
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 6 days ago by
Ram
39k • written 6 days ago by
Mah
• 0
1
vote
3
replies
221
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
mls
• 0
0
votes
0
replies
109
views
snpEff error. No CDS checked
snpEff
gtf
WES
6 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
111
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
6 days ago by
Maddie
• 0
1
vote
2
replies
209
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
5 days ago by
rheab1230
▴ 140
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 6 days ago by
Ram
39k • written 6 days ago by
miguellarrazlopezdenovales
• 0
2
votes
4
replies
323
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
5 days ago by
Kiran
▴ 80
0
votes
0
replies
105
views
Count hexamer bias from pair end short read data
short
DESeq2
bias
read
hexamer
updated 6 days ago by
rpolicastro
12k • written 6 days ago by
Jjbox
▴ 40
1
vote
0
replies
107
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
6 days ago by
fr
▴ 200
3
votes
3
replies
280
views
Can any one suggest tools that generate "mind-maps" on concepts in biology/biotech?
Mind-maps
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 6 days ago by
John Erik
• 0
3
votes
2
replies
149
views
Panther db Reference List
pantherdb
enrichment-tests
updated 6 days ago by
Ram
39k • written 6 days ago by
e.r.zakiev
▴ 50
0
votes
2
replies
175
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 6 days ago by
rpolicastro
12k • written 6 days ago by
Pac314
▴ 10
0
votes
1
reply
126
views
ABO alleles
ABO
variants
SNPs
alleles
updated 6 days ago by
Raony Guimarães
★ 1.2k • written 6 days ago by
Fernando
• 0
1
vote
1
reply
151
views
How to determine the exact version of hg38 if I have only the FASTA file
reference-genome
FASTA
updated 6 days ago by
Ram
39k • written 6 days ago by
mps
• 0
0
votes
2
replies
167
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 days ago by
survive
• 0
1
vote
1
reply
129
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
hashim.rana11
▴ 20
2
votes
1
reply
167
views
sctransform on scRNA seq
seurat
updated 6 days ago by
ATpoint
72k • written 7 days ago by
friguiahlem8
▴ 10
1
vote
4
replies
194
views
Dot Plot using KEGG
KEGG
DotPlot
GO
6 days ago by
smanzano250800
• 0
13
votes
25
replies
3.0k
views
7 follow
VEP output has no gene names
alignment
sequencing
vep
updated 6 days ago by
barslmn
★ 1.6k • written 4.8 years ago by
Gene_MMP8
▴ 230
0
votes
23
replies
443
views
gatk Hardfilter Error
hardfilter
updated 6 days ago by
Michael
52k • written 7 days ago by
bestone
▴ 10
3
votes
3
replies
185
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
updated 6 days ago by
andres.firrincieli
3.4k • written 7 days ago by
Sebastian Hesse
▴ 320
1
vote
7
replies
286
views
Docker Error while running nf-core/rnaseq pipeline
RNA-seq
nf-core
docker
updated 6 days ago by
ATpoint
72k • written 7 days ago by
eesha28112001
• 0
2
votes
3
replies
176
views
What type of normalization did they use in this article?
normalization
TPM
r
updated 6 days ago by
Ram
39k • written 7 days ago by
JACKY
▴ 100
2
votes
4
replies
203
views
MACS2 peak calling
MACS2
peak-calling
updated 6 days ago by
seidel
11k • written 7 days ago by
Maurice
• 0
1
vote
1
reply
157
views
Which type of variant caller should I use in a WES normal cell line sample?
variant-caller
WES
updated 7 days ago by
ATpoint
72k • written 7 days ago by
bompipi95
▴ 120
9
votes
8
replies
301
views
Alignment of case vs. control from different origin
Alignment
RNAseq
3 hours ago by
sativus
▴ 10
0
votes
2
replies
242
views
Peaks annotation on bacterial genome
ChIPpeakAnno
annotation
bacteria
7 days ago by
Maurice
• 0
1,000 results • Page
4 of 20
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs
by
GenoMax
129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
Yeah, I added the design matrix. `design <- model.matrix(~0+group)`. The `counts` is log2-normalized raw data.
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Ayish
• 0
Thank you for reply. I have Illumina paired-end reads. Would it be fine if I use hard-masking for STAR and soft-masked genome for BRAKER2? …
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
Soft masking the genome (unless something changed) not make any difference for STAR. Depending on how your RNA-Seq is done (Illumina? paire…
Answer: How to handle NaN in emmax Kinship matrix?
by
Thu
• 0
Hi! Thanks for sharing your solution! It works! :)
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