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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
3
replies
249
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 8 days ago by
GenoMax
141k • written 8 days ago by
neish
• 0
1
vote
0
replies
148
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 8 days ago by
Ram
43k • written 8 days ago by
ian.will
▴ 30
0
votes
0
replies
101
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
8 days ago by
nhaus
▴ 300
1
vote
3
replies
258
views
True variants selection
vcf
bcftools
updated 7 days ago by
dthorbur
★ 1.9k • written 8 days ago by
maevalefeuvre
• 0
0
votes
1
reply
150
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
CY
▴ 750
0
votes
0
replies
100
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
8 days ago by
JirMan
▴ 20
1
vote
1
reply
165
views
Failed to download data from EBI with ascp
EBI
aspera
updated 8 days ago by
GenoMax
141k • written 9 days ago by
biock
▴ 60
0
votes
0
replies
390
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
9 days ago by
Isaac
• 0
0
votes
0
replies
100
views
Combining VG graphs
vg
graphs
combine
9 days ago by
AshleeThomson
▴ 70
0
votes
0
replies
105
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 8 days ago by
Ram
43k • written 9 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
176
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 9 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Saran
▴ 50
0
votes
2
replies
260
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
7 days ago by
ramin.k2013
• 0
0
votes
0
replies
154
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 8 days ago by
Ram
43k • written 9 days ago by
ramin.k2013
• 0
0
votes
1
reply
158
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 9 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
sainavyav22
• 0
0
votes
9
replies
554
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 8 days ago by
LauferVA
4.2k • written 9 days ago by
Aki
▴ 10
0
votes
0
replies
89
views
Issue while using circle_dat function from GOplot in R
GOplot
R
9 days ago by
ckelly96
• 0
0
votes
2
replies
180
views
Can't figure out plink --sample-diff
plink
9 days ago by
curious
▴ 750
0
votes
1
reply
136
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 9 days ago by
GenoMax
141k • written 9 days ago by
Reno
• 0
1
vote
2
replies
205
views
convert a seurat object to expressionset
Seurat
9 days ago by
Bine
▴ 60
2
votes
4
replies
379
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 9 days ago by
GenoMax
141k • written 10 days ago by
pl.terzian
• 0
0
votes
0
replies
111
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
9 days ago by
txema.heredia
▴ 110
0
votes
0
replies
97
views
cibersortx colnames
gema122
9 days ago by
gem1
• 0
0
votes
2
replies
211
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
7 days ago by
marongiu.luigi
▴ 710
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 10 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
0
replies
97
views
Confused about the results of a function in dada2 pipeline sample inference step
Microbiome
R
dada2
10 days ago by
Mohamed Samir
▴ 20
1
vote
4
replies
788
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
10 days ago by
Hyper_Odin
▴ 310
2
votes
4
replies
274
views
Addmetadata to seurat obj
seurat
9 days ago by
synat.keam
▴ 100
0
votes
0
replies
96
views
Methylation array analysis using dmpFinder
epic
methylation
normalization
dmp
mset
10 days ago by
Roy
▴ 10
0
votes
0
replies
183
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
10 days ago by
rijan_dhakal2055
• 0
0
votes
5
replies
377
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 9 days ago by
GenoMax
141k • written 10 days ago by
Shay
• 0
2
votes
2
replies
222
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
9 days ago by
javanokendo
▴ 60
0
votes
0
replies
99
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
10 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
228
views
Problem with downloading genome in SnpEff
SnpEff
9 days ago by
Javier
• 0
0
votes
0
replies
101
views
Comparison between Bracken outputs
Bracken
Kraken
Taxonomy
10 days ago by
SushiRoll
▴ 120
0
votes
4
replies
257
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
9 days ago by
njornet
▴ 20
0
votes
0
replies
115
views
DESeq2 LRT divergent DEGs ?
interaction
LRT
deseq2
10 days ago by
klervi-lugue
• 0
0
votes
2
replies
210
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
10 days ago by
neish
• 0
0
votes
3
replies
258
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 10 days ago by
joe
▴ 510 • written 10 days ago by
CrisRisu
• 0
0
votes
1
reply
152
views
P-values for pairwise FST
FST
P-value
pairwise
updated 10 days ago by
dthorbur
★ 1.9k • written 11 days ago by
Emy
▴ 50
0
votes
4
replies
320
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 8 days ago by
GenoMax
141k • written 11 days ago by
Soohyun
• 0
0
votes
0
replies
233
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 11 days ago by
Ram
43k • written 11 days ago by
sooni
▴ 20
0
votes
0
replies
136
views
Seurat Package
seurat
11 days ago by
odi
▴ 10
0
votes
0
replies
114
views
RUVg correction
differential-expression
ruvseq
updated 10 days ago by
Ram
43k • written 11 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
117
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
10 days ago by
Chris
▴ 260
0
votes
0
replies
129
views
Methylation workflow problem
rstudio
methylation
updated 11 days ago by
Ram
43k • written 11 days ago by
Roy
▴ 10
0
votes
0
replies
127
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
11 days ago by
Thomas
• 0
2
votes
2
replies
246
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
4 days ago by
bioinfo
▴ 150
0
votes
5
replies
492
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 11 days ago by
Ram
43k • written 15 days ago by
Greg
• 0
0
votes
1
reply
196
views
Pattern of GC content across reads from fastp
multiqc
ddRAD
updated 11 days ago by
GenoMax
141k • written 11 days ago by
jberg
• 0
2
votes
6
replies
381
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
11 days ago by
jkim
▴ 170
1,000 results • Page
3 of 20
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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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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