Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
231 results • Page
4 of 5
Sort: Votes
Rank
Views
Votes
Replies
0
votes
2
replies
286
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
0
votes
0
replies
99
views
Merging Hi-C datasets originating from experiments using different enzymes
enzymes
Hi-C
updated 1 day ago by
Ram
43k • written 1 day ago by
hamarillo
▴ 70
0
votes
4
replies
248
views
Parsing fasta file by coordinates
linux
fasta
updated 1 hour ago by
Joe
21k • written 2 days ago by
sorrymouse
▴ 120
0
votes
0
replies
163
views
Tutorial:
Parsing HMMER output
HMMER
updated 5 days ago by
GenoMax
140k • written 5 days ago by
I0110
▴ 130
0
votes
0
replies
99
views
Convert VCF file and add covariate information
VCF
PED
PLINK
1 day ago by
asmariyaz23
▴ 10
0
votes
4
replies
225
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
1 hour ago by
rohitsatyam102
▴ 840
0
votes
3
replies
297
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv
compressing
varscan
bcftools
5 days ago by
kabir.deb
▴ 80
0
votes
0
replies
99
views
bulk RNA-seq: how to remove batch effect between multiple batches and labels?
combat
batch
1 day ago by
kiraqueen
• 0
0
votes
0
replies
163
views
working with shapeit.
shapeit
6 days ago by
sanchit000singhdr098
• 0
0
votes
0
replies
170
views
scRNA Cell Clustering Defined by Normalized Counts
Normalization
scRNA
Seurat
6 days ago by
sakura
• 0
0
votes
1
reply
30
views
ONT direct RNA sequencing
gz
DRS
ONT
gunzip
gzip
updated 1 hour ago by
dthorbur
★ 1.7k • written 1 hour ago by
Karina
• 0
0
votes
1
reply
136
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 1 day ago by
ATpoint
81k • written 1 day ago by
David Arturo
• 0
0
votes
1
reply
141
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
0
votes
0
replies
155
views
Motif Scanning: HOMER vs MEME, settings?
homer
fimo
6 days ago by
mb
• 0
0
votes
0
replies
164
views
How to identify the phylogenetic node age of RNAs?
phylogeny
genome
evolution
RNA-seq
6 days ago by
Apex92
▴ 280
0
votes
9
replies
428
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 1 hour ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
9
replies
452
views
Intersect genomic locations with genes
fanc
Chromatin
conformation
Hic
hic
updated 6 days ago by
zx8754
11k • written 6 days ago by
naveedhasan2000
• 0
0
votes
0
replies
90
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
0
replies
10
views
How to change alternate conformation occupancy ?
Module
Bio.PDB.Atom
Bio.PDB
updated 37 minutes ago by
GenoMax
140k • written 38 minutes ago by
udakshi
• 0
0
votes
4
replies
355
views
bcftools select sites with multiple combinations of FILTER column
bcftools
6 days ago by
User000
▴ 690
0
votes
0
replies
82
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
0
replies
75
views
GSEA number dimension of expression dataset
GSEA
23 hours ago by
edoardofilippi1998
• 0
0
votes
0
replies
74
views
Creating a custom ontology for peptides
ontology
peptide
22 hours ago by
Mathew
• 0
0
votes
3
replies
210
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
22 hours ago by
sarahmanderni
▴ 100
0
votes
1
reply
404
views
Get_Homologues
get_homologues
homologues
clusters
updated 22 hours ago by
b.contreras.moreira
▴ 70 • written 5 months ago by
utkarsh.sood
▴ 40
0
votes
2
replies
214
views
Using the Ontology Lookup Service (OLS) API
API
OLS
22 hours ago by
longoka
▴ 40
0
votes
1
reply
113
views
How can I remove duplicate SNP?
plink
updated 22 hours ago by
iraun
6.2k • written 22 hours ago by
Zhennan
• 0
0
votes
0
replies
77
views
Number of pathway result from GSVA
GSVA
22 hours ago by
Chris
▴ 260
0
votes
2
replies
210
views
Limma compare between 3 conditions vs 2 conditions
Limma
22 hours ago by
Chris
▴ 260
0
votes
3
replies
386
views
RNAseq
R
RNA-seq
Linux
6 days ago by
mrymrahimi70
• 0
0
votes
0
replies
178
views
Questions on demultiplexing using Qiime2
demultiplexing
barcode
6 days ago by
Minh
• 0
0
votes
2
replies
148
views
Error with goodSamplesGenes()
R
WGCNA
20 hours ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
100
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 20 hours ago by
Yogi
▴ 70 • written 21 hours ago by
Ronin
• 0
0
votes
2
replies
289
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 20 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
0
replies
77
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 20 hours ago by
Ram
43k • written 21 hours ago by
r.shiasi3897
▴ 10
0
votes
1
reply
126
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 19 hours ago by
Ram
43k • written 22 hours ago by
Hajar
• 0
0
votes
0
replies
183
views
Problem encountered during Pearson Correlation Analysis between two immune cell subtypes
scRNA-seq
biostatistics
6 days ago by
applepie
• 0
0
votes
6
replies
406
views
Download Panther entry list
PANTHER
6 days ago by
Nicolas
• 0
0
votes
1
reply
28
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 58 minutes ago by
ATpoint
81k • written 1 hour ago by
gdfsnkfns
• 0
0
votes
4
replies
332
views
HISAT2 installation issue
HISAT2
updated 6 days ago by
GenoMax
140k • written 6 days ago by
eleven11
• 0
0
votes
4
replies
495
views
calculating mean fragment length from CollectInsertSizeMetrics(Picard) output
count2fpkm
updated 6 days ago by
ATpoint
81k • written 10 days ago by
Niharika
• 0
0
votes
1
reply
91
views
Update R in Posit Workbench
R
Posit
updated 17 hours ago by
Ram
43k • written 17 hours ago by
Nitin
• 0
0
votes
1
reply
105
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 16 hours ago by
Mensur Dlakic
★ 26k • written 23 hours ago by
Ricard
• 0
0
votes
2
replies
151
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
15 hours ago by
Ankit
▴ 500
0
votes
7
replies
308
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 14 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
0
replies
72
views
doing some ontology enrichment analysis
GO
14 hours ago by
aleksk779
• 0
0
votes
1
reply
467
views
Which fasta files are assembled transcripts IDBA_tran assembler ?
RNA-Seq
Assembly
updated 13 hours ago by
weidonglu
• 0 • written 3.8 years ago by
sunnykevin97
▴ 980
0
votes
5
replies
379
views
Issues filtering VCF file with bcftools/vcftools
vcftools
vcf
bcftools
updated 6 days ago by
Pierre Lindenbaum
160k • written 21 days ago by
ekirsch
• 0
0
votes
2
replies
141
views
novel and know mir156 and mir172
a
updated 13 hours ago by
gayachit
▴ 200 • written 16 hours ago by
Fadmo
• 0
0
votes
8
replies
510
views
Fine-tuning NCBI taxid / taxidlist
BLAST
taxonomy
6 days ago by
theclubstyle
▴ 40
231 results • Page
4 of 5
Recent Votes
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
Comment: Issue with making local BLAST database
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Recent Locations •
All
Russia,
just now
Slovenia,
1 minute ago
Germany,
1 minute ago
France/Nantes/Institut du Thorax - INSERM UMR1087,
1 minute ago
Nepal,
1 minute ago
United States,
2 minutes ago
United Kingdom,
3 minutes ago
Recent Awards •
All
Popular Question
to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
Popular Question
to
beacamara
• 0
Scholar
to
Devon Ryan
104k
Popular Question
to
blur
▴ 280
Popular Question
to
ATpoint
81k
Teacher
to
Haci
▴ 550
Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
Traffic: 2476 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6