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119,663 results • Page
6 of 2394
Sort: Rank
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0
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118
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Germline CNV CALLING
gErmline
CNV
updated 15 days ago by
GenoMax
147k • written 16 days ago by
Smilesky
• 0
0
votes
0
replies
111
views
Packages for constructing Phylogenetic tree from HapMap file
HapMap
tree
Phylogenetic
SNP
16 days ago by
sujee119
• 0
3
votes
5
replies
2.7k
views
How Do I create a BED file from an hard masked fasta?
genome
sequencing
updated 16 days ago by
hewm2008
▴ 50 • written 5.5 years ago by
marcofraca
▴ 20
3
votes
1
reply
346
views
What is the reason that all high throughput sequencing data for the human brain is snRNA-seq instead of scRNA-seq ?
10x
scanpy
python
single-cell
anndata
updated 16 days ago by
jared.andrews07
★ 18k • written 16 days ago by
JACKY
▴ 160
1
vote
2
replies
281
views
Picard LiftoverVCF Maps Variants to Incorrect Chromosomes When Processing Individual Chromosomes
liftovervcf
16 days ago by
jonas.andersson
▴ 40
0
votes
0
replies
123
views
News:
Master Evidence Synthesis with Meta-analysis in R (Online Course - Feb 10-14, 2025)
Meta-analysis
Review
Evidence-Synthesis
16 days ago by
Physalia-courses
★ 2.6k
0
votes
3
replies
327
views
PCA plot
fviz_pca
factoextra
updated 15 days ago by
Bastien Hervé
5.9k • written 16 days ago by
4732b159
• 0
6
votes
8
replies
890
views
NGS data analysis
NGS
eukaryotic
13 days ago by
Acervo
• 0
0
votes
0
replies
128
views
Intersect between bedGraph and bed file
count
bedtools
bedGraph
Matrix
16 days ago by
daffodil
▴ 10
1
vote
0
replies
378
views
is there any data base or reference to provide a comprehensive list of CD marker expression in different white blood cell types?
DEG
myeloid
CDmarker
leukocyte
16 days ago by
qasemi.m.q
▴ 10
1
vote
2
replies
346
views
How to interpret that overrepresented and duplicate sequences influence %GC content?
Duplicates
FASTQC
MultiQC
Fastq
GC
14 days ago by
tvibhaps
▴ 10
0
votes
0
replies
127
views
Should we normalize/transform WGBS beta values?
normalization
WGBS
methylation
transfromation
17 days ago by
Lalaland
▴ 40
0
votes
4
replies
589
views
What is the best way to confirm if a mutated gene is more frequent in recurrence group than in baseline?
statistics
compare_groups
gene_count
17 days ago by
Lila M
★ 1.3k
0
votes
0
replies
169
views
How to combine replicates in profile plot in profileplyr package?
ATAC-Seq
profilePlot
profilePlyr
updated 17 days ago by
GenoMax
147k • written 18 days ago by
B.N.
▴ 10
0
votes
2
replies
385
views
No Cluster ID's present when making UMAP for Joint RNA and ATAC analysis: Signac 10x multiomic tutorial
multiomics
snATACseq
snRNAseq
18 days ago by
bgbs
• 0
0
votes
0
replies
174
views
Phasing alleles with SHAPEIT4: cases and controls together or separately?
cases-controls
separately
together
case-control
phasing
18 days ago by
igor.alcaras
• 0
2
votes
1
reply
1.8k
views
Is it better to phase two populations together or separately?
phasing
beagle
populations
updated 18 days ago by
igor.alcaras
• 0 • written 9.0 years ago by
eyb
▴ 270
0
votes
3
replies
399
views
Clarification with vcf file
quality
vcf
VCF
score
updated 17 days ago by
GenoMax
147k • written 18 days ago by
Nesma
• 0
2
votes
8
replies
1.0k
views
SRAtoolkit --split-files output
sratoolkit
sra
fastq
18 days ago by
tony_88888
• 0
0
votes
1
reply
287
views
m6A modification prediction using Nanopore DRS data (RNA004)
m6A
DRS
Nanopore
updated 17 days ago by
GenoMax
147k • written 18 days ago by
baibhu1234
• 0
0
votes
0
replies
179
views
database of gmap file for GLIMPSE2 imputation
gmap
GLIMPSE2
18 days ago by
cautree
• 0
3
votes
6
replies
653
views
Create a fasta and gtf file
gtf
human
genome
fasta
updated 17 days ago by
Juke34
8.9k • written 18 days ago by
ATRX
★ 1.1k
1
vote
2
replies
328
views
Regarding to Two-color microarray data analysis (DGE)
Differential-expression-analysis
updated 18 days ago by
Ram
44k • written 19 days ago by
SHIRUI
▴ 10
11
votes
12
replies
1.3k
views
dedup STAR transcriptome file using umi_tools
rna-seq
umi
transcriptome
umi_tools
18 days ago by
ATRX
★ 1.1k
0
votes
1
reply
223
views
ChIP-seq signal values
values
chipseq
signal
updated 18 days ago by
1769mkc
★ 1.2k • written 18 days ago by
SEJAL
• 0
0
votes
0
replies
199
views
Speclib of Rattus novergicus (taxid 10116) to use in DIA-NN
Proteomics
19 days ago by
thalisommoreiraskt
• 0
0
votes
1
reply
288
views
News:
[Survey] Help Shape the Future of Genomic Data Storage Solutions!
genomics
bioinformatics
survey
solutions
storage
updated 18 days ago by
Michael
55k • written 19 days ago by
spacecow
• 0
1
vote
1
reply
282
views
QQ plot with small bump in the middle
QQ-plot.GWAS
updated 18 days ago by
Ram
44k • written 19 days ago by
zhuzhu
▴ 10
4
votes
3
replies
441
views
Confused by reference files
reference
alignment
updated 19 days ago by
GenoMax
147k • written 19 days ago by
Nesma
• 0
3
votes
4
replies
482
views
Contrasts for comparing condition within tissue
limma
deseq2
edgeR
contrasts
updated 18 days ago by
SamGG
▴ 70 • written 19 days ago by
Ben
▴ 20
1
vote
2
replies
383
views
How to Map NCBI taxid to Open Tree of Life ott_id Without Using Scientific Names?
taxonomy
ott
19 days ago by
Martín Ezequiel
• 0
0
votes
2
replies
288
views
Cellranger: Demux pooled (hashing antibodies) GEX and VDJ 10x sequence fastq data
hashing
cellranger
demux
19 days ago by
Flipstone
• 0
11
votes
2
replies
528
views
Tutorial:
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda
Anaconda
license
19 days ago by
Juke34
8.9k
0
votes
0
replies
212
views
Fixed peak width in ENCODE TFs ChIP-seq
MACS2
ChIP-seq
ENCODE
19 days ago by
DavideBrex
▴ 20
0
votes
0
replies
220
views
vg call AD frequencies for certain sites
vg
19 days ago by
Danny
• 0
2
votes
2
replies
456
views
Job:
Research Scientist - Bioinformatics position in Milan, Italy
R
Python
RNASeq
singleCell
19 days ago by
kanika.151
▴ 160
0
votes
3
replies
369
views
Questions about finding similar genes and dissimilar genes in BLAST
E-value
similarity
BLAST
updated 19 days ago by
biofalconch
★ 1.3k • written 20 days ago by
William
• 0
1
vote
3
replies
545
views
Question about variant calling method using pangenome-graph
vg
updated 7 days ago by
Jouni Sirén
▴ 470 • written 20 days ago by
Marion
• 0
0
votes
1
reply
281
views
Are there specific pipelines for identifying solo-TIRs?
solo-TIR
elements
transposable
updated 19 days ago by
biofalconch
★ 1.3k • written 20 days ago by
Marcos
▴ 10
3
votes
5
replies
565
views
Optical Duplicates
gatk
MarkDuplicates
optical-duplicates
updated 5 days ago by
Ram
44k • written 20 days ago by
ebogen
▴ 10
4
votes
2
replies
453
views
Tool:
A notebook for checking relatedness and X heterozygosity from sequencing data
heterozygosity
relatedness
sequencing
sex
estimation
19 days ago by
barslmn
★ 2.3k
0
votes
0
replies
234
views
Signac for mgatk scRNA-seq data
mgatk
Signac
scRNA-seq
20 days ago by
marco.barr
▴ 150
0
votes
0
replies
225
views
Homer annotatePeaks.pl output
start
annotatePeaks.pl
chr
homer
position
updated 20 days ago by
GenoMax
147k • written 20 days ago by
Rakesh
• 0
1
vote
2
replies
378
views
Extract gene_id and protein_id from .gtf file to create a list with them
gtf
bash
protein_id
20 days ago by
Eduardo Oñate
• 0
0
votes
0
replies
219
views
GEOquery getGEO is normalized data or not?
getgeo
geoquery
microarray
20 days ago by
tyasird
▴ 10
27
votes
35
replies
3.0k
views
Indexing a 2.6GB Plant Genome Using STAR (genomeGenerate Mode) Terminated Due to RAM Limit — Can the Genome Be Split for Indexing, or Are There Other…
star
RAN-seq
bam
genome
indexing
updated 14 hours ago by
Dunois
★ 2.8k • written 21 days ago by
Vijith
▴ 90
1
vote
3
replies
428
views
Tool:
I Built a Simple Website to Help Researchers find Research Grants
web-application
grants
research
funding
updated 20 days ago by
GenoMax
147k • written 20 days ago by
bitsofadventures
▴ 40
4
votes
1
reply
350
views
Differential Expression Analysis with only one replicate
Differential-Expression-analysis
updated 20 days ago by
Ram
44k • written 21 days ago by
ZuelTech
• 0
4
votes
7
replies
582
views
Basic de novo assembly of plant genome
Assembly
updated 19 days ago by
lieven.sterck
15k • written 21 days ago by
Lemonhope
▴ 10
0
votes
4
replies
601
views
TCGAbiolinks - fewer samples than expected
TCGABiolinks
TCGA
updated 15 days ago by
Zhenyu Zhang
★ 1.2k • written 4 months ago by
elmira.yazdii
• 0
119,663 results • Page
6 of 2394
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Comment: Could Anyone Help Me with Seurat code
Comment: BBMap Excess Fold Coverage
Answer: STAR alignment for RNA seq - trouble occurred
Answer: RNA-seq's strange genes
Comment: Converting gene_ids from GTF file to common gene symbols
Comment: Converting gene_ids from GTF file to common gene symbols
Answer: Why higher read counts in chromosome M/MT
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Answer: STAR alignment for RNA seq - trouble occurred
by
Alex
• 0
P address 161.52.190.122
Comment: STAR alignment for RNA seq - trouble occurred
by
ohtang7
▴ 40
Thank you so much! After using the genome_unmasked file from Ensembl that you mentioned, I was able to get results for around 25,000 genes.…
Comment: Add contig lenght to VCF header in a robust way
by
Lhl
▴ 760
Hi Jena, It seems bcftools reheader utility does not work the way showed in your example. ``` bcftools reheader About: Modify header o…
Comment: RNA-seq's strange genes
by
SeoG
• 0
Thank you for your answer.
Answer: Generating multiple species reference for CellRanger
by
LChart
4.6k
A prefix for ensembl genes is not necessary. ENSG is strictly human; other species have different prefixes (ENSSSCG for the pig reference).…
Comment: Converting gene_ids from GTF file to common gene symbols
by
Gus
• 0
Awesome! Thank you -- I really appreciate all the expertise on this forum
Comment: Converting gene_ids from GTF file to common gene symbols
by
LChart
4.6k
You can query the protein name in UniProt: `https://rest.uniprot.org/uniprotkb/search?query=protein_name:"multiple epidermal growth factor…
Comment: Converting gene_ids from GTF file to common gene symbols
by
Gus
• 0
Well, I've successfully mapped my NCBI gene_ids to the other file's gene_ids and annotation info, but I still am lacking common gene symbol…
Comment: DE analysis from kallisto estimated counts (only)
by
dsull
★ 6.9k
The abundance.tsv is the raw kallisto output -- is there any reason that you can't get the abundance.tsv files? Running kallisto automatica…
Comment: Clustal omega on M1 Mac
by
GenoMax
147k
See if the answer here helps: https://www.biostars.org/p/128261/#128406
Comment: how to choose cufflinks library type from infer_experiment
by
GenoMax
147k
See: https://www.biostars.org/p/295344/ In second case that looks like an unstranded library.
Answer: IGV large deletions
by
wakaruszka
▴ 20
Hello. The red paired reads indicate that their insert size is unexpectedly large after mapping to the reference genome. This can be expla…
Answer: Why higher read counts in chromosome M/MT
by
wakaruszka
▴ 20
Hi. What you are actually seeing are not tandem duplicate reads. Note that the human mitochondrial genome is circular, but in IGV the r…
Comment: Converting gene_ids from GTF file to common gene symbols
by
Gus
• 0
I'll give that a shot. Thanks!
Comment: Converting gene_ids from GTF file to common gene symbols
by
LChart
4.6k
> The NCBI .gtf file has an attribute "orig_transcript_id" with features like "gnl|WGS:JAMFTG|CAt00007278.1". The last string contains the …
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