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116,011 results • Page
1 of 2321
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How to change alternate conformation occupancy ?
Module
Bio.PDB.Atom
Bio.PDB
updated just now by
GenoMax
140k • written 1 minute ago by
udakshi
• 0
0
votes
0
replies
6
views
Training
chip-seq
ScATAC-seq
13 minutes ago by
Manhezz
• 0
1
vote
1
reply
21
views
Issue with making local BLAST database
database
mitochodrial
diatoms
blast
ncbi
9 minutes ago by
Begonia_pavonina
▴ 140
1
vote
1
reply
222
views
diffbind : killed dba.count(DBsample, bParallel=FALSE)
diffbind
r
atacseq
49 minutes ago by
Pierre Lindenbaum
160k
0
votes
1
reply
24
views
ONT direct RNA sequencing
gz
DRS
ONT
gunzip
gzip
updated 55 minutes ago by
dthorbur
★ 1.7k • written 1 hour ago by
Karina
• 0
0
votes
1
reply
21
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 27 minutes ago by
ATpoint
81k • written 1 hour ago by
gdfsnkfns
• 0
1
vote
8
replies
57
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
3 minutes ago by
Lila M
★ 1.2k
793
votes
167
replies
139k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.6k • written 7.3 years ago by
Istvan Albert
100k
0
votes
1
reply
31
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Pumla
• 0
0
votes
1
reply
47
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 2 hours ago by
andrebolerbarros
• 0 • written 2 hours ago by
Christian
• 0
0
votes
1
reply
48
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 1 hour ago by
Ram
43k • written 2 hours ago by
Mohamed Abderrahmane
• 0
0
votes
0
replies
29
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
2 hours ago by
Broccoli
• 0
0
votes
0
replies
32
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
3 hours ago by
blur
▴ 280
0
votes
0
replies
42
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
3 hours ago by
liuyibin2005
• 0
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 19 minutes ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
0
votes
0
replies
34
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial
SPOTlight
transcriptomic
logFC
deconvolution
4 hours ago by
M'zelle
• 0
0
votes
3
replies
126
views
calculate mismatch rate from VCF file
rate
VCF
mismatch
updated 1 hour ago by
Pierre Lindenbaum
160k • written 10 hours ago by
Dora
▴ 10
0
votes
1
reply
47
views
Downloading a list of all refseq assembly ids, including supressed assembliey
refseq
ncbi
assembly
updated 44 minutes ago by
GenoMax
140k • written 4 hours ago by
Bertalan_Takacs
▴ 90
2
votes
3
replies
254
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
updated 4 hours ago by
colindaven
6.3k • written 2 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
122
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
updated 6 hours ago by
kayah
• 0 • written 8 hours ago by
Nitin
• 0
0
votes
0
replies
52
views
In scRNA, How should I set QC standards?
scRNA
QC
6 hours ago by
mnx0723
• 0
0
votes
0
replies
45
views
Annotation of Complex genomes using NCBI Genome Workbench
annotation
Genome
MAKER
Workbench
8 hours ago by
SAsciences
• 0
0
votes
2
replies
222
views
Error occurs when migrate-n software performs "make mpis"
migrate-n
9 hours ago by
lingxue
• 0
0
votes
0
replies
56
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
10 hours ago by
Chris
▴ 260
1
vote
10
replies
692
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 9 hours ago by
GenoMax
140k • written 5 weeks ago by
Sky
▴ 10
3
votes
2
replies
261
views
FDR and Bonferroni
FDR
Bonferroni
updated 10 hours ago by
joe
▴ 470 • written 2 days ago by
song
• 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
0
replies
70
views
doing some ontology enrichment analysis
GO
13 hours ago by
aleksk779
• 0
2
votes
1
reply
163
views
Choosing an FC Threshold
statistics
rna-seq
updated 13 hours ago by
Gordon Smyth
★ 6.9k • written 1 day ago by
Netanel
• 0
0
votes
1
reply
104
views
Converting AutoDock-Vina PDBQTs to PDB files
Docking
AutoDock
Vina
PDBQT
PDB
updated 16 hours ago by
Mensur Dlakic
★ 26k • written 22 hours ago by
Ricard
• 0
0
votes
2
replies
140
views
novel and know mir156 and mir172
a
updated 12 hours ago by
gayachit
▴ 200 • written 16 hours ago by
Fadmo
• 0
0
votes
1
reply
90
views
Update R in Posit Workbench
R
Posit
updated 17 hours ago by
Ram
43k • written 17 hours ago by
Nitin
• 0
2
votes
8
replies
229
views
Piping samtools to R
R
NGS
bash
samtools
17 hours ago by
joe
▴ 470
8
votes
6
replies
377
views
Pangenome of plant
pangenome
plant
updated 19 hours ago by
talbots
• 0 • written 1 day ago by
analyst
▴ 10
1
vote
2
replies
170
views
vg call is time consuming
vg
18 hours ago by
Maxine
▴ 40
4
votes
14
replies
4.5k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 19 hours ago by
Ram
43k • written 21 months ago by
Elsa
▴ 20
0
votes
8
replies
393
views
STAR aligner options
STAR
2 hours ago by
theophile
• 0
2
votes
3
replies
502
views
Website or tool to obtain a list of genes that participate in a specific process?
genomics
updated 20 hours ago by
NancyTLi
• 0 • written 3 months ago by
Hamtaro
▴ 50
0
votes
2
replies
289
views
How to obtain Node/ Edge information from a Reactome Pathway
R
API
pathways
reactome
databases
updated 19 hours ago by
GenoMax
140k • written 4 weeks ago by
K.patel5
▴ 140
0
votes
2
replies
150
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
14 hours ago by
Ankit
▴ 500
0
votes
1
reply
99
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 19 hours ago by
Yogi
▴ 70 • written 20 hours ago by
Ronin
• 0
0
votes
0
replies
75
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 19 hours ago by
Ram
43k • written 21 hours ago by
r.shiasi3897
▴ 10
0
votes
0
replies
76
views
Number of pathway result from GSVA
GSVA
21 hours ago by
Chris
▴ 260
0
votes
1
reply
111
views
How can I remove duplicate SNP?
plink
updated 21 hours ago by
iraun
6.2k • written 22 hours ago by
Zhennan
• 0
0
votes
1
reply
124
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
73
views
Creating a custom ontology for peptides
ontology
peptide
22 hours ago by
Mathew
• 0
0
votes
3
replies
195
views
convert cds to seurat object
R
monocle3
seurat
updated 1 hour ago by
edoardofilippi1998
• 0 • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
74
views
GSEA number dimension of expression dataset
GSEA
22 hours ago by
edoardofilippi1998
• 0
0
votes
2
replies
210
views
Limma compare between 3 conditions vs 2 conditions
Limma
21 hours ago by
Chris
▴ 260
0
votes
0
replies
82
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
116,011 results • Page
1 of 2321
Recent Votes
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
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Recent Replies
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: Downloading a list of all refseq assembly ids, including supressed assembliey
by
GenoMax
140k
Can you provide examples of suppressed ID's?
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…
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