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489 results • Page
4 of 10
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Votes
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0
votes
2
replies
257
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
11 days ago by
DKA
▴ 40
0
votes
0
replies
166
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
14 days ago by
Hien
• 0
0
votes
2
replies
297
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
12 days ago by
Koketso
• 0
0
votes
0
replies
194
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 14 days ago by
Ram
43k • written 14 days ago by
menyawino
• 0
1
vote
3
replies
362
views
Ensembl gene id conversion
biomart
ensembl
updated 12 days ago by
ATpoint
82k • written 14 days ago by
naveedhasan2000
• 0
1
vote
2
replies
322
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 13 days ago by
Istvan Albert
100k • written 15 days ago by
Jiang
• 0
0
votes
0
replies
196
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
15 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
322
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
15 days ago by
O.rka
▴ 710
0
votes
6
replies
558
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
13 days ago by
Dunois
★ 2.5k
4
votes
7
replies
565
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 15 days ago by
Ram
43k • written 16 days ago by
AHerik
▴ 20
0
votes
0
replies
192
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 16 days ago by
GenoMax
141k • written 16 days ago by
zec018
• 0
0
votes
0
replies
194
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 16 days ago by
Ram
43k • written 16 days ago by
roussine
▴ 10
0
votes
0
replies
183
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
16 days ago by
Ronin
• 0
4
votes
13
replies
883
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 12 days ago by
BioinfGuru
★ 1.7k • written 17 days ago by
matteo.levorato
• 0
2
votes
1
reply
251
views
VEP annotation --per_gene allele choice
VEP
updated 16 days ago by
Ram
43k • written 16 days ago by
atariw
▴ 10
0
votes
2
replies
289
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 16 days ago by
Zhenyu Zhang
★ 1.2k • written 16 days ago by
Apollonia
• 0
1
vote
1
reply
250
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 16 days ago by
Ram
43k • written 16 days ago by
Fish
• 0
0
votes
0
replies
187
views
Snakemake fails to find conda in PBS
snakemake
16 days ago by
yixinzeng
• 0
0
votes
0
replies
189
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
16 days ago by
Mary
• 0
0
votes
0
replies
182
views
Protein stability analysis
mutation
analysis
16 days ago by
marco.barr
▴ 80
1
vote
4
replies
398
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 15 days ago by
BioinfGuru
★ 1.7k • written 16 days ago by
Morteza
• 0
3
votes
1
reply
268
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 17 days ago by
Ram
43k • written 17 days ago by
rj.rezwan
• 0
0
votes
0
replies
172
views
Multiple Spike-Ins
MeRIP
Spike-In
17 days ago by
Adam
▴ 30
0
votes
0
replies
161
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 17 days ago by
Ram
43k • written 17 days ago by
Reno
• 0
2
votes
2
replies
277
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
161
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
17 days ago by
eesiribloom
▴ 80
0
votes
3
replies
325
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 15 days ago by
ATpoint
82k • written 17 days ago by
gdfsnkfns
• 0
0
votes
4
replies
326
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
17 days ago by
me
• 0
0
votes
2
replies
268
views
WGCNA
PCA
WGCNA
EIGENGENE
17 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
272
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 17 days ago by
GenoMax
141k • written 17 days ago by
neish
• 0
1
vote
0
replies
159
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 17 days ago by
Ram
43k • written 17 days ago by
ian.will
▴ 30
0
votes
0
replies
108
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
17 days ago by
nhaus
▴ 310
1
vote
3
replies
286
views
True variants selection
vcf
bcftools
updated 16 days ago by
dthorbur
★ 1.9k • written 17 days ago by
maevalefeuvre
• 0
0
votes
1
reply
168
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 17 days ago by
Ram
43k • written 17 days ago by
CY
▴ 750
0
votes
0
replies
110
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
17 days ago by
JirMan
▴ 20
1
vote
1
reply
176
views
Failed to download data from EBI with ascp
EBI
aspera
updated 17 days ago by
GenoMax
141k • written 17 days ago by
biock
▴ 60
0
votes
0
replies
399
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
17 days ago by
Isaac
• 0
0
votes
0
replies
109
views
Combining VG graphs
vg
graphs
combine
18 days ago by
AshleeThomson
▴ 80
0
votes
0
replies
116
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 17 days ago by
Ram
43k • written 18 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
186
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
Saran
▴ 50
0
votes
2
replies
275
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
16 days ago by
ramin.k2013
• 0
0
votes
0
replies
163
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 17 days ago by
Ram
43k • written 18 days ago by
ramin.k2013
• 0
0
votes
1
reply
177
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
sainavyav22
• 0
0
votes
9
replies
596
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 17 days ago by
LauferVA
4.2k • written 18 days ago by
Aki
▴ 20
0
votes
0
replies
98
views
Issue while using circle_dat function from GOplot in R
GOplot
R
18 days ago by
ckelly96
• 0
0
votes
2
replies
202
views
Can't figure out plink --sample-diff
plink
18 days ago by
curious
▴ 750
0
votes
1
reply
154
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 18 days ago by
GenoMax
141k • written 18 days ago by
Reno
• 0
1
vote
2
replies
226
views
convert a seurat object to expressionset
Seurat
17 days ago by
Bine
▴ 60
2
votes
4
replies
404
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 18 days ago by
GenoMax
141k • written 19 days ago by
pl.terzian
• 0
0
votes
0
replies
122
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
18 days ago by
txema.heredia
▴ 110
489 results • Page
4 of 10
Recent Votes
Comment: PDB related issue
Comment: PDB related issue
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
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Popular Question
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Zhenyu Zhang
★ 1.2k
Popular Question
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WUSCHEL
▴ 750
Teacher
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Mensur Dlakic
★ 27k
Teacher
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Jeremy Leipzig
22k
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Recent Replies
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
I reinstalled nodejs: > sudo apt-get install nodejs Its already up to date with version v10.19.0
Answer: NGS forensics: how to know if data is fabricated
by
Prash
▴ 270
Mensur, if I were you, I'd probably contact the CA directly and check with him whether they have reproduced the works recently. There coul…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 550
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
• 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
Gordon Smyth
★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated
by
benformatics
3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue
by
noodle
▴ 550
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue
by
Mensur Dlakic
★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
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