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121,935 results • Page
127 of 2439
Sort: Rank
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Votes
Replies
0
votes
0
replies
705
views
Problem with GATK FilterMutectCalls : using contamination table doesn' t change anything
vcf
contaminationtable
gatk
filtermutectcalls
genomics
18 months ago by
Samuel
▴ 20
0
votes
8
replies
2.2k
views
FreeBayes encountered a sudden error
freebayes
updated 18 months ago by
Michael
56k • written 18 months ago by
emilydolivo97
▴ 10
0
votes
1
reply
570
views
Quantify the junction abundance?
TCGA
splicing-junction
updated 18 months ago by
Zhenyu Zhang
★ 1.3k • written 18 months ago by
lm
• 0
0
votes
3
replies
922
views
lncRNA from TCGA
lihc
tcga
lncrna
updated 18 months ago by
ATpoint
89k • written 18 months ago by
jain72744
▴ 10
0
votes
1
reply
591
views
How do I know whether it is not a failure of ChIPseq data
ChIPseq
updated 17 months ago by
dthorbur
★ 3.1k • written 18 months ago by
Herman Einstein
• 0
8
votes
6
replies
1.7k
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
18 months ago by
yuanj
▴ 40
1
vote
2
replies
932
views
Bioinformatics variant calling software
variant-calling
updated 18 months ago by
Jeremy Leipzig
23k • written 18 months ago by
cFll
• 0
0
votes
0
replies
453
views
Saccharomyces cerevisiae orthologs in plants
database
orthologs
18 months ago by
dec986
▴ 380
0
votes
4
replies
1.2k
views
Gene Ontology question
differential-expression
Gene-ontology
updated 17 months ago by
Ram
45k • written 18 months ago by
Bhawna
• 0
0
votes
0
replies
351
views
Looking for Comprehensive Virtual Screening Examples with Results Validation
drug-discovery
virtual-screening
molecular-docking
updated 18 months ago by
Ram
45k • written 18 months ago by
Stefano
• 0
0
votes
1
reply
559
views
samflags to removes mapped concordantly >1 times
samtools
Bowtie2
Metagenome
updated 17 months ago by
jkbonfield
★ 1.3k • written 18 months ago by
pompam_5904
• 0
4
votes
2
replies
931
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
Lee
• 0
0
votes
0
replies
394
views
TransDecoder ORF score to filter "noise" from de novo transcriptome assembly
transdecoder
assembly
transcriptome
updated 18 months ago by
Ram
45k • written 18 months ago by
tdamiani
• 0
1
vote
2
replies
773
views
Problem with SRA
SRA
updated 18 months ago by
Ram
45k • written 18 months ago by
Daniel
• 0
0
votes
0
replies
359
views
Should I keep taxa that have 0 counts when calculating alpha diversity?
Shannon-Weiner
18 months ago by
DNAngel
▴ 260
0
votes
1
reply
1.5k
views
How to do DE between cells expressing specific gene in scanpy?
scRNA-seq
single-cell
scanpy
updated 18 months ago by
Ram
45k • written 18 months ago by
bioinfo
▴ 160
0
votes
5
replies
1.3k
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 18 months ago by
GenoMax
154k • written 18 months ago by
Sony
▴ 20
7
votes
8
replies
3.3k
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
18 months ago by
Riq
▴ 50
1
vote
4
replies
1.3k
views
UniProt accession number
protein
UniProt
updated 18 months ago by
Elisabeth Gasteiger
★ 2.4k • written 18 months ago by
1204079053
• 0
5
votes
3
replies
11k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 18 months ago by
far
▴ 10 • written 7.3 years ago by
Volka
▴ 180
0
votes
1
reply
1.3k
views
MMSeqs2 Removing Redundancy
mmseqs
mmseqs2
updated 18 months ago by
GenoMax
154k • written 18 months ago by
dthorbur
★ 3.1k
1
vote
7
replies
17k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 18 months ago by
Vassilis
• 0 • written 11.5 years ago by
liu4gre
▴ 210
0
votes
0
replies
273
views
Transcription Factor Binding sites intersecting Transposable Elements
TE
TFBP
18 months ago by
M.Adiba
• 0
2
votes
5
replies
1.3k
views
WGCNA website
wgcna
updated 18 months ago by
GenoMax
154k • written 18 months ago by
Dave Carlson
★ 2.2k
2
votes
2
replies
1.9k
views
What is the relationship between Illumina P5 P7, universal adapters, and TruSeq Adapter Index 7?
fastqc
NGS
18 months ago by
octpus616
▴ 120
0
votes
4
replies
1.6k
views
kmer analysis for genome size estimation
kmer
merqury
allotetraploid
pacbio
hifiasm
18 months ago by
rj.rezwan
▴ 20
0
votes
5
replies
1.1k
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
18 months ago by
virginia.baraja
• 0
5
votes
3
replies
2.3k
views
Problems with Nextflow to run NanoRtax Pipeline
NanoRtax
Nextflow
Nanopore
updated 18 months ago by
colindaven
8.0k • written 18 months ago by
kerianaleerivera
▴ 10
0
votes
1
reply
785
views
How plot multiple enrichment plot together
singlecell
updated 18 months ago by
dthorbur
★ 3.1k • written 18 months ago by
synat.keam
▴ 120
2
votes
5
replies
1.0k
views
Tool to Identify Gene, Regulatory Role, and Function at Integration Sites
chromosome
regulatory
integration
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
kelpotus22
• 0
0
votes
0
replies
380
views
Extracting tcga images for cnn in r
rstudio
python
tcga-lihc
svs
18 months ago by
jain72744
▴ 10
2
votes
4
replies
1.1k
views
filtering VCF sites and impose whatever excluded ad missing
conditions
vcf
filters
bcftools
18 months ago by
Matteo Ungaro
▴ 130
0
votes
3
replies
840
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 18 months ago by
Ram
45k • written 18 months ago by
atharvakarkare14
▴ 40
0
votes
7
replies
1.5k
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 18 months ago by
Papyrus
★ 3.1k • written 18 months ago by
doramora
▴ 10
0
votes
0
replies
747
views
Looking to improve my understanding of Homer's mergePeaks function: unclear of how the merged file is created?
Homer
ATACseq
18 months ago by
Ronin
▴ 10
1
vote
4
replies
2.0k
views
cloupe to 10x format
seurat
10X
cloupe
updated 18 months ago by
Ram
45k • written 18 months ago by
M'zelle
• 0
0
votes
1
reply
1.3k
views
How do I annotate a ggtree object with bootstrap values?
ggtree
phylogenetic-tree
R
bootstrap
updated 18 months ago by
inedraylig
▴ 70 • written 18 months ago by
Yarabi
• 0
2
votes
9
replies
1.5k
views
frequency of each variant per sample
freebayes
variant-frequency
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
emilydolivo97
▴ 10
0
votes
2
replies
829
views
Azure vs AWS for cloud computing with Kraken2?
aws
azure
metagenomics
kraken2
written 2.1 years ago by
Natalia
• 0
0
votes
0
replies
442
views
RobustRankAggreg rankMatrix subscript out of boundaries
RobustRankAggreg
microarray
R
rankMatrix
18 months ago by
hagl
▴ 20
1
vote
3
replies
5.4k
views
MSF Data Analysis
MSF
Proteomics
Thermo
Proteome Discoverer
updated 18 months ago by
Bioinformatics_16
• 0 • written 5.8 years ago by
JJDollar
▴ 130
0
votes
1
reply
479
views
Meta analysis of transcriptomic data
Meta-analysis
18 months ago by
Raman
• 0
0
votes
3
replies
1.1k
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
17 months ago by
JY
• 0
0
votes
0
replies
312
views
Handling data from RNA-seq experiement with negative cell controls / Water samples
rnaseq
18 months ago by
kvn95ss
▴ 20
0
votes
1
reply
607
views
Large differences in Differentially expressed genes between two datasets.
PPI
STRING
Cytoscape
DEGs
updated 18 months ago by
Scooter
▴ 310 • written 18 months ago by
rijul
• 0
0
votes
0
replies
340
views
Seurat-DE analysis
seurat
DE
18 months ago by
odi
▴ 10
0
votes
1
reply
592
views
sorted bam file generated from gff transcript fastas, how to get counts with HTseq?
htseq
bam
updated 18 months ago by
Ram
45k • written 18 months ago by
RNAseqer
▴ 280
1
vote
5
replies
1.1k
views
samtools filtering
samtools
updated 17 months ago by
jkbonfield
★ 1.3k • written 18 months ago by
san96
▴ 190
3
votes
2
replies
3.3k
views
Fail to install umap-learn in R
cellchat
R
updated 18 months ago by
Ram
45k • written 19 months ago by
synat.keam
▴ 120
3
votes
4
replies
3.0k
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness
contamination
18 months ago by
beacamara
• 0
121,935 results • Page
127 of 2439
Recent Votes
Answer: how to explain the sample size discrepancy in UCSC Xena
Answer: Linear regression vs DESeq2 models for DEG analysis
C: how to format the featurecounts output ?
C: how to format the featurecounts output ?
What happened to biomart.org
Answer: allele frequency in VCF
Understanding terms, specifically relating to GT:PL in a VCF file
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Recent Replies
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
curious
▴ 890
Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run.…
Comment: how to explain the sample size discrepancy in UCSC Xena
by
nuorain
▴ 40
Thank you very much.
Answer: how to explain the sample size discrepancy in UCSC Xena
by
i.sudbery
22k
Because there wasn't RNA-seq analysis performed for every sample in TCGA?
Answer: Linear regression vs DESeq2 models for DEG analysis
by
i.sudbery
22k
There are two main problems with using linear models for read-count based analyses. Firstly, linear models assume a normal distribution…
Comment: real time PCR data analysis
by
ATpoint
89k
I cannot guide on GraphPad. It's commercial software so better contact their support.
Answer: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
Comment: What happened to biomart.org
by
Jeremy Leipzig
23k
same with geuvadis.org
Comment: real time PCR data analysis
by
Gordon Smyth
★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction
by
Fatemeh
▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis
by
Fatemeh
▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org
by
GenoMax
154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
GenoMax
154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis
by
ATpoint
89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org
by
ATpoint
89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction
by
Fatemeh
▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
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