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523 results • Page
3 of 11
Sort: replies
Rank
Views
Votes
Replies
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 20 days ago by
Ram
43k • written 2.8 years ago by
K
▴ 10
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 10 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 8 days ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
3
replies
279
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
18 days ago by
Jeyong
• 0
1
vote
3
replies
248
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 20 days ago by
Ram
43k • written 2.3 years ago by
matt81rd
▴ 10
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
2
votes
3
replies
254
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 23 days ago by
Ram
43k • written 24 days ago by
Netanel
• 0
0
votes
3
replies
613
views
Not all variants are annotated with AF - expected or a problem?
Variant-Calling
WGS
Alignment
updated 23 days ago by
Ram
43k • written 7 months ago by
Luiz
▴ 30
1
vote
3
replies
347
views
Ensembl gene id conversion
biomart
ensembl
updated 10 days ago by
ATpoint
82k • written 12 days ago by
naveedhasan2000
• 0
0
votes
3
replies
261
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
29 days ago by
sarahmanderni
▴ 100
0
votes
3
replies
583
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
28 days ago by
Nitin
• 0
1
vote
3
replies
351
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 24 days ago by
Pierre Lindenbaum
161k • written 26 days ago by
Max
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 7 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
3
votes
3
replies
316
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
26 days ago by
Pumla
• 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 7 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
0
votes
3
replies
320
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 13 days ago by
ATpoint
82k • written 14 days ago by
gdfsnkfns
• 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 16 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
0
votes
3
replies
446
views
How do I get the gene annotations as a text file from a genbank file?
sequence-annotation
genbank
updated 27 days ago by
Ram
43k • written 28 days ago by
eae6d2e7
• 0
0
votes
3
replies
261
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 14 days ago by
GenoMax
141k • written 15 days ago by
neish
• 0
0
votes
3
replies
261
views
can't download and use mageck-vispr for R?
mageck-vispr
Rstudio
updated 24 days ago by
ATpoint
82k • written 24 days ago by
Vishal
• 0
0
votes
3
replies
170
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 5 hours ago by
Pierre Lindenbaum
161k • written 8 hours ago by
J
• 0
1
vote
3
replies
389
views
multiple sequence alignment
BLAST
multiple-sequence-alignment
clustal-omega
MSA
updated 17 days ago by
Ram
43k • written 20 days ago by
catherinemaria2728
• 0
1
vote
3
replies
276
views
True variants selection
vcf
bcftools
updated 14 days ago by
dthorbur
★ 1.9k • written 15 days ago by
maevalefeuvre
• 0
0
votes
3
replies
337
views
Resources regarding Proteomics (In-Silico)
molecular-simulation
docking
protein
proteomics
updated 24 days ago by
Ram
43k • written 5 weeks ago by
Saurabh
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 7 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 9 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
0
votes
3
replies
217
views
Peptide identification from Mass spec data
Transcriptomics
Proteins
Mass-spec
updated 21 days ago by
Ram
43k • written 22 days ago by
atharvakarkare14
▴ 10
0
votes
3
replies
265
views
rRNA depletion of RIP-seq samples
rRNA
RIP-seq
updated 16 days ago by
joe
▴ 510 • written 17 days ago by
CrisRisu
• 0
0
votes
3
replies
305
views
Help with mauve
mauve
updated 20 days ago by
Ram
43k • written 7 weeks ago by
reachedahead225
• 0
1
vote
2
replies
202
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
17 days ago by
phhelou5
• 0
0
votes
2
replies
264
views
RNAseq 1 control 2 different treatment
RNA-seq
10 days ago by
matteo.levorato
• 0
2
votes
2
replies
630
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 9 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
0
votes
2
replies
578
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 20 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
0
votes
2
replies
245
views
Problem with downloading genome in SnpEff
SnpEff
15 days ago by
Javier
• 0
0
votes
2
replies
236
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
0
votes
2
replies
316
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
12 days ago by
O.rka
▴ 710
0
votes
2
replies
258
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 9 days ago by
Ram
43k • written 10 days ago by
David
• 0
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 9 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 9 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
0
votes
2
replies
534
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
7 days ago by
航太郎
• 0
0
votes
2
replies
266
views
WGCNA
PCA
WGCNA
EIGENGENE
14 days ago by
rajasekargutha
▴ 60
0
votes
2
replies
70
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 hour ago by
GenoMax
141k • written 4 hours ago by
sapuizait
▴ 10
1
vote
2
replies
327
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 23 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 20 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
0
votes
2
replies
209
views
novel and know mir156 and mir172
a
updated 29 days ago by
gayachit
▴ 200 • written 29 days ago by
Fadmo
• 0
1
vote
2
replies
315
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 10 days ago by
Istvan Albert
100k • written 12 days ago by
Jiang
• 0
1
vote
2
replies
922
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 20 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
523 results • Page
3 of 11
Recent Votes
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Converting between Ensembl Versions
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Answer: what is the purpose of indexing the reference genome (Kallisto)
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How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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If you have the accession numbers can you not use something like `eutils`?
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> Next, I tried using bedtools window but in your original post you said > tried finding the intersection of these bed files using bedto…
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Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
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> using bcftools Show us what you tried
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