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816 results • Page
3 of 17
Sort: replies
Rank
Views
Votes
Replies
3
votes
5
replies
1.7k
views
Remap GRCh38.p13 to GRCh38
haplotype
bed
genome
freeze
map
updated 6 days ago by
Jeremy Leipzig
21k • written 2.2 years ago by
schmau
▴ 10
0
votes
5
replies
443
views
convert data frame with character column to data frame with integer column
r
updated 2 days ago by
Basti
★ 1.6k • written 5 days ago by
atemedorri137798
• 0
6
votes
5
replies
9.6k
views
Forum:
Single-end sequencing versus paired-end
Assembly
snp
sequencing
updated 6 hours ago by
Ram
39k • written 3.3 years ago by
Sujata
▴ 20
5
votes
5
replies
3.5k
views
How to create SAF from text file for FeatureCounts
featureCounts
ATAC-seq
updated 6 hours ago by
Ram
39k • written 2.1 years ago by
pt.taklifi
▴ 60
0
votes
5
replies
392
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 5 days ago by
Joe
21k • written 5 days ago by
gunala.nikhil
• 0
2
votes
5
replies
1.6k
views
NarrowPeak format -Peak field
ChIP-Seq
dnase-seq
bed
updated 6 days ago by
ATpoint
72k • written 2.7 years ago by
kimkes25
▴ 50
14
votes
5
replies
6.1k
views
Forum:
Seurat vs Monocle
R
RNA-Seq
next-gen
single-cell
updated 6 days ago by
Ram
39k • written 3.9 years ago by
Arup Ghosh
3.2k
1
vote
5
replies
899
views
Correct reference for Platinum Genomes?
genome
sequencing
updated 6 hours ago by
Ram
39k • written 3.3 years ago by
Tails
▴ 80
6
votes
5
replies
1.5k
views
Forum:
Stanford HCP MS Biomedical Informatics vs Johns Hopkins MS Bioinformatics
career
updated 6 hours ago by
Ram
39k • written 3.3 years ago by
melissachua90
▴ 40
4
votes
5
replies
594
views
how to design a guide RNA
genomics
updated 5 days ago by
rfran010
▴ 170 • written 18 days ago by
Bioinfo
• 0
3
votes
5
replies
2.9k
views
GISTIC 2.0 markers
segmentation
marker
cnv
gistic
updated 5 days ago by
Ram
39k • written 3.7 years ago by
enho
▴ 40
0
votes
5
replies
324
views
All combinations of two columns R
R
updated 5 days ago by
Ram
39k • written 5 days ago by
Fernando
• 0
0
votes
5
replies
955
views
bigwigs to reads in peaks
R
atac-seq
updated 6 hours ago by
Ram
39k • written 2.4 years ago by
pt.taklifi
▴ 60
6
votes
5
replies
5.3k
views
BWA aln - failed to locate the index
alignment
bwa
updated 5 days ago by
Ram
39k • written 3.7 years ago by
m.wekking
▴ 10
6
votes
5
replies
807
views
Job:
Collaboration for phd thesis
next-gen
updated 8 hours ago by
Ram
39k • written 3.4 years ago by
Hope AKKARI
▴ 10
1
vote
5
replies
1.6k
views
Wrong coordinates of peaks in DiffBind
DiffBind
ATAC-seq
updated 6 hours ago by
Ram
39k • written 4.7 years ago by
grant.hovhannisyan
★ 2.5k
0
votes
5
replies
84
views
VCF file CSQ flag
vcf
exome-sequencing
updated 2 hours ago by
Ram
39k • written 4 hours ago by
Payal
▴ 140
1
vote
5
replies
387
views
Is a human genome file with reference as NCBI37 the same as hg19?
vcf
hg19
genome
reference-genome
updated 3 days ago by
GenoMax
130k • written 4 days ago by
a5864557
• 0
4
votes
5
replies
827
views
Forum:
A silly question about journal clubs
journal-club
challenge
updated 4 hours ago by
Ram
39k • written 3.3 years ago by
flogin
▴ 280
6
votes
5
replies
6.3k
views
Forum:
Converting GFF to GTF
GTF
GFF
updated 3 hours ago by
Ram
39k • written 3.2 years ago by
Juke34
7.9k
6
votes
5
replies
1.1k
views
7 follow
Forum:
What do you think of sci-hub?
sci-hub
updated 1 day ago by
Ram
39k • written 3.4 years ago by
cduukj
• 0
6
votes
4
replies
971
views
How does long reads help in the repeated regions of the genome
Illumina
short-reads
long-reads
ONT
updated 5 hours ago by
Ram
39k • written 2.7 years ago by
Ashi
▴ 20
8
votes
4
replies
1.6k
views
News:
supporting vg users on biostars
variation-graph
genome
vg
vgteam
updated 5 days ago by
Ram
39k • written 3.7 years ago by
Erik Garrison
★ 2.4k
11
votes
4
replies
345
views
how to sort a fasta file
fasta
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
Mohd
▴ 20
0
votes
4
replies
206
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
2 days ago by
amy__
▴ 50
4
votes
4
replies
295
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 6 days ago by
ATpoint
72k • written 6 days ago by
bioinfo
▴ 80
3
votes
4
replies
231
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 9 hours ago by
Ram
39k • written 1 day ago by
shamza
• 0
4
votes
4
replies
1.6k
views
how to identify disease variants from bam file ?
disease-variants
VCF
bam
ATAC-seq
updated 6 hours ago by
Ram
39k • written 4.5 years ago by
masaver
▴ 20
4
votes
4
replies
889
views
Forum:
Kubernetes in Production?
ci-cd
webservice
kubernetes
docker
updated 1 day ago by
Ram
39k • written 3.5 years ago by
acamukhin
• 0
0
votes
4
replies
281
views
Identification of genes involved in my pathway
KEGG
keggGet
6 days ago by
smanzano250800
• 0
2
votes
4
replies
309
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 40 minutes ago by
Rory Stark
★ 1.8k • written 2 days ago by
B.N.
• 0
2
votes
4
replies
1.4k
views
What is the best way to analyze and enrich a list of DE genes from RNAseq?
R
pathways
enrichment
RNA-Seq
updated 2 hours ago by
Ram
39k • written 3.2 years ago by
mario.red8976
▴ 110
7
votes
4
replies
1.1k
views
Forum:
Studying for a Bioinformatics degree
sequence
R
next-gen
gene
RNA-Seq
updated 8 hours ago by
Ram
39k • written 3.4 years ago by
O'kin-1
▴ 20
2
votes
4
replies
264
views
Get relationships and hierarchies for GO terms
GO-terms
Gene-onthology
updated 1 day ago by
Alexander
▴ 70 • written 2 days ago by
DanielEB_fisk
▴ 10
5
votes
4
replies
789
views
IQ-TREE stuck in selecting a substitution model with ModelFinder
substitution
ModelFInder
model
IQ-TREE
updated 16 hours ago by
rohitsatyam102
▴ 690 • written 10 months ago by
Begonia_pavonina
▴ 100
0
votes
4
replies
5.0k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 2 days ago by
Franco
• 0 • written 5.6 years ago by
ac.research
▴ 30
1
vote
4
replies
194
views
Dot Plot using KEGG
KEGG
DotPlot
GO
6 days ago by
smanzano250800
• 0
7
votes
4
replies
406
views
Forum:
[Meta] Use of AI
AI
Artificial-Intelligence
meta
ChatGPT
updated 2 days ago by
Ram
39k • written 4 days ago by
Vincent Laufer
★ 2.9k
3
votes
4
replies
281
views
Gene prediction software
pseudogene
gene
prediction
masking
updated 14 hours ago by
Darked89
4.4k • written 1 day ago by
subashini.fbtpb106
▴ 20
2
votes
4
replies
823
views
Downloading all the heteroComplex protein PDB IDs in RCSB Protein Data Bank
python
biopython
updated 2 days ago by
Ram
39k • written 3.6 years ago by
Christian
• 0
1
vote
4
replies
229
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
2 days ago by
Daniel
▴ 30
3
votes
4
replies
4.7k
views
How to get the gene expression matrix from GEO while getGEO returns 0 features?
GETquery
ATAC-seq
GEO
getGEO
RNA-Seq
updated 6 hours ago by
Ram
39k • written 3.9 years ago by
bioyas
▴ 10
1
vote
4
replies
64
views
How to get information about promoter from bulk-RNAseq?
promoter
R
RNA-seq
2 hours ago by
camillab.
▴ 130
1
vote
4
replies
466
views
best annotation approach for peaks
chipseeker
R
chippeakanno
updated 5 days ago by
rfran010
▴ 170 • written 23 days ago by
Chironex
▴ 40
2
votes
4
replies
811
views
Anybody knows any stand alone tool/pipeline for Bacterial Gene Ontology (GO) analysis?
gene
genome
sequence
updated 6 hours ago by
Ram
39k • written 2.7 years ago by
Kumar
▴ 100
2
votes
4
replies
110
views
Differences in GTF files hg19 and hg38
hg38
hg19
GTF
updated 3 hours ago by
GenoMax
130k • written 7 hours ago by
heureuse
• 0
2
votes
4
replies
323
views
PacBio Pipeline and Tools for Variant Call
longread
pacbio
whatshap
pbmm2
5 days ago by
Kiran
▴ 80
1
vote
4
replies
1.7k
views
Algorithm for clustering single cells based on SNPs?
10x-genomics
SNP
single-cell
updated 2 days ago by
Ram
39k • written 3.6 years ago by
A248
▴ 10
9
votes
4
replies
3.8k
views
Difference between Allele frequency spectrum and Joint allele frequency spectrum
allele
population structure
updated 5 days ago by
jena
▴ 260 • written 5.1 years ago by
beausoleilmo
▴ 530
13
votes
4
replies
984
views
Forum:
The shortcoming of shiny app in building webserver
R
shiny
webserver
updated 5 days ago by
Ram
39k • written 3.7 years ago by
harrypotterandsbt
▴ 110
816 results • Page
3 of 17
Recent Votes
NM_transcript ID gene identification
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
A: Mouse promoter regions
Answer: How to get information about promoter from bulk-RNAseq?
A: Extracting Flanking Regions across TSS using R scripts
A: Mouse promoter regions
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Recent Replies
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
> One idea is to provide just the representative sequences as a first > pass. This seems reasonable since it should capture significant pa…
Comment: pal2nal -nogap -nomismatch options not working
by
Marie
• 0
Hi, did you end up solving this? I am running into the same issue. Marie
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
and what about enhancer? is it possible to do it from a bulk-RNAseq?
Comment: How to get information about promoter from bulk-RNAseq?
by
camillab.
▴ 130
yes! clearly the terminology on my side needs to improved!
Comment: How to get information about promoter from bulk-RNAseq?
by
rpolicastro
12k
Generally speaking, most promoters only initiate transcription for a single gene, with a single gene potentially having multiple promoters …
Answer: How to get information about promoter from bulk-RNAseq?
by
Trivas
★ 1.2k
I'd probably select the genes of interest from your bulk RNA-seq results then use the UCSC table browser to get the sequence upstream of th…
Comment: How to add annotation columns with specific colors to the heatmap?
by
Ram
39k
Show us your exact code - it is quite easy to tweak colors in ComplexHeatmap with the `col=` argument.
Comment: VCF file CSQ flag
by
Ram
39k
True, but it's not technically impossible to annotate GVCFs, which is why I did not address that point.
Comment: Creating a local version of Clustered NR database
by
PeterC_NCBI
▴ 260
@genomax Sorry for the delay in reply. We're still working out the details of what exactly to provide. One idea is to provide just the rep…
Comment: Shannon's Entropy by Sliding Window in R
by
rohitsatyam102
▴ 690
Hi Were u able to achieve this?
Comment: Differences in GTF files hg19 and hg38
by
GenoMax
130k
Since this is not an answer to the original question do not add it as such. I moved your last comment to the correct spot it should have be…
Comment: VCF file CSQ flag
by
Pierre Lindenbaum
154k
if your talking about the gvcf produced by HaplotypeCaller with ERC=GVCF, you don't annote g.vcf files , you must first merge the g.vcf.f…
Comment: [python]sklearn.ensemble.RandomForestClassifier(TypeError: string indices must b
by
Ram
39k
https://www.biostars.org/u/127538/ : Please delete this question or it will be deleted by moderators in a few days.
Comment: VCF file CSQ flag
by
Ram
39k
A gvcf files has blocks for both variant loci and non-variant loci, so you won't see a CSQ for each record, only for those variant loci wit…
Comment: Differences in GTF files hg19 and hg38
by
heureuse
• 0
Thank you very much. I get it from UCSC.
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