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1,000 results • Page
4 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
309
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
13 days ago by
me
• 0
0
votes
2
replies
262
views
WGCNA
PCA
WGCNA
EIGENGENE
12 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
256
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 13 days ago by
GenoMax
141k • written 13 days ago by
neish
• 0
1
vote
0
replies
154
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 13 days ago by
Ram
43k • written 13 days ago by
ian.will
▴ 30
0
votes
0
replies
103
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
13 days ago by
nhaus
▴ 300
1
vote
3
replies
271
views
True variants selection
vcf
bcftools
updated 12 days ago by
dthorbur
★ 1.9k • written 13 days ago by
maevalefeuvre
• 0
0
votes
1
reply
157
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 13 days ago by
Ram
43k • written 13 days ago by
CY
▴ 750
0
votes
0
replies
107
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
13 days ago by
JirMan
▴ 20
1
vote
1
reply
172
views
Failed to download data from EBI with ascp
EBI
aspera
updated 13 days ago by
GenoMax
141k • written 13 days ago by
biock
▴ 60
0
votes
0
replies
394
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
13 days ago by
Isaac
• 0
0
votes
0
replies
106
views
Combining VG graphs
vg
graphs
combine
13 days ago by
AshleeThomson
▴ 80
0
votes
0
replies
111
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 13 days ago by
Ram
43k • written 13 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
182
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 13 days ago by
Pierre Lindenbaum
161k • written 13 days ago by
Saran
▴ 50
0
votes
2
replies
269
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
11 days ago by
ramin.k2013
• 0
0
votes
0
replies
159
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 13 days ago by
Ram
43k • written 13 days ago by
ramin.k2013
• 0
0
votes
1
reply
171
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 14 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
sainavyav22
• 0
0
votes
9
replies
576
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 12 days ago by
LauferVA
4.2k • written 14 days ago by
Aki
▴ 10
0
votes
0
replies
93
views
Issue while using circle_dat function from GOplot in R
GOplot
R
14 days ago by
ckelly96
• 0
0
votes
2
replies
189
views
Can't figure out plink --sample-diff
plink
14 days ago by
curious
▴ 750
0
votes
1
reply
146
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 14 days ago by
GenoMax
141k • written 14 days ago by
Reno
• 0
1
vote
2
replies
215
views
convert a seurat object to expressionset
Seurat
13 days ago by
Bine
▴ 60
2
votes
4
replies
392
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 14 days ago by
GenoMax
141k • written 15 days ago by
pl.terzian
• 0
0
votes
0
replies
118
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
14 days ago by
txema.heredia
▴ 110
0
votes
0
replies
100
views
cibersortx colnames
gema122
14 days ago by
gem1
• 0
0
votes
2
replies
219
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
12 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 14 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
0
replies
99
views
Confused about the results of a function in dada2 pipeline sample inference step
Microbiome
R
dada2
14 days ago by
Mohamed Samir
▴ 20
1
vote
4
replies
806
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
14 days ago by
Hyper_Odin
▴ 310
2
votes
4
replies
291
views
Addmetadata to seurat obj
seurat
14 days ago by
synat.keam
▴ 100
0
votes
0
replies
100
views
Methylation array analysis using dmpFinder
epic
methylation
normalization
dmp
mset
15 days ago by
Roy
▴ 10
0
votes
0
replies
188
views
Confused by the `--ld-window` flag in Vcftools. What does the number of SNPs between SNPs mean?
tabix
vcftools
15 days ago by
rijan_dhakal2055
• 0
0
votes
5
replies
396
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 14 days ago by
GenoMax
141k • written 15 days ago by
Shay
• 0
0
votes
0
replies
102
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
15 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
238
views
Problem with downloading genome in SnpEff
SnpEff
14 days ago by
Javier
• 0
0
votes
0
replies
109
views
Comparison between Bracken outputs
Bracken
Kraken
Taxonomy
15 days ago by
SushiRoll
▴ 120
0
votes
4
replies
272
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
14 days ago by
njornet
▴ 20
0
votes
0
replies
120
views
DESeq2 LRT divergent DEGs ?
interaction
LRT
deseq2
15 days ago by
klervi-lugue
• 0
0
votes
2
replies
218
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
14 days ago by
neish
• 0
0
votes
3
replies
261
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 15 days ago by
joe
▴ 510 • written 15 days ago by
CrisRisu
• 0
0
votes
1
reply
159
views
P-values for pairwise FST
FST
P-value
pairwise
updated 15 days ago by
dthorbur
★ 1.9k • written 15 days ago by
Emy
▴ 50
0
votes
4
replies
329
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 13 days ago by
GenoMax
141k • written 15 days ago by
Soohyun
• 0
0
votes
0
replies
250
views
batch correction: cds from seurat
batch-correction
R
seurat
monocle3
cds
updated 15 days ago by
Ram
43k • written 15 days ago by
sooni
▴ 20
0
votes
0
replies
138
views
Seurat Package
seurat
15 days ago by
odi
▴ 10
0
votes
0
replies
116
views
RUVg correction
differential-expression
ruvseq
updated 15 days ago by
Ram
43k • written 15 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
123
views
How to annotate pairwise p value from limma (3 groups) in a combine multiple boxplot?
limma
boxplot
15 days ago by
Chris
▴ 260
0
votes
0
replies
131
views
Methylation workflow problem
rstudio
methylation
updated 16 days ago by
Ram
43k • written 16 days ago by
Roy
▴ 10
0
votes
0
replies
129
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
16 days ago by
Thomas
• 0
2
votes
2
replies
256
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
8 days ago by
bioinfo
▴ 150
0
votes
5
replies
520
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 16 days ago by
Ram
43k • written 19 days ago by
Greg
• 0
0
votes
1
reply
201
views
Pattern of GC content across reads from fastp
multiqc
ddRAD
updated 15 days ago by
GenoMax
141k • written 16 days ago by
jberg
• 0
1,000 results • Page
4 of 20
Recent Votes
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
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Recent Replies
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM
by
swbarnes2
14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt
by
barslmn
★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
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