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116,668 results • Page
1 of 2334
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0
votes
3
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594
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Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated just now by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
74
views
Perfom a Gene Ontology Analysis from GO terms txt file
GO
RNASeq
updated 58 minutes ago by
sansan_96
▴ 80 • written 2 hours ago by
Hamtaro
▴ 50
0
votes
0
replies
25
views
Polishing genome assembly
polishing
Nanopore
PacBio
2 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
67
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 2 hours ago by
LChart
3.9k • written 7 hours ago by
kl
▴ 10
0
votes
1
reply
57
views
Differential Accessibility
DiffBind
updated 2 hours ago by
Ram
43k • written 3 hours ago by
Shloka
• 0
0
votes
1
reply
75
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 3 hours ago by
GenoMax
141k • written 4 hours ago by
kim
• 0
2
votes
2
replies
226
views
Extract protein sequence
fasta
alignment
blast
3 hours ago by
anna
▴ 20
0
votes
3
replies
190
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 7 hours ago by
noodle
▴ 570 • written 19 hours ago by
WUSCHEL
▴ 750
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
4
replies
170
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 4 hours ago by
Wayne
★ 2.0k • written 10 hours ago by
Mariana
▴ 10
0
votes
1
reply
76
views
metagenomic virome quality assessment
viromics
metagenomics
updated 7 hours ago by
Ram
43k • written 11 hours ago by
Petchimuthu
• 0
3
votes
7
replies
191
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
6 hours ago by
salias
• 0
0
votes
0
replies
43
views
Using limma in methylation EM-seq?
EM-seq
methylation
8 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
480
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
8 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
53
views
Synteny analysis
bacterial
synteny
genome
updated 8 hours ago by
GenoMax
141k • written 9 hours ago by
Namil
• 0
0
votes
2
replies
90
views
Genbank File Format
gbkformat
updated 8 hours ago by
Mensur Dlakic
★ 27k • written 9 hours ago by
alenew.am
• 0
0
votes
5
replies
301
views
How should I make kallisto indexes?
kallisto
updated 7 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
89
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
9 hours ago by
SSSJec
• 0
0
votes
3
replies
135
views
Software to separate reads from different individuals
software
development
nanopore
updated 5 hours ago by
GenoMax
141k • written 9 hours ago by
njornet
▴ 20
0
votes
0
replies
47
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
10 hours ago by
David
• 0
4
votes
5
replies
188
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 10 hours ago by
dsull
★ 5.9k • written 13 hours ago by
Kazo
▴ 10
0
votes
2
replies
107
views
How to update R on ubuntu
installation
update
R
apt-get
9 hours ago by
Bosberg
▴ 50
3
votes
0
replies
71
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
11 hours ago by
Biostar
2.7k
0
votes
1
reply
93
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 12 hours ago by
GenoMax
141k • written 16 hours ago by
Ruqaiya
• 0
0
votes
1
reply
244
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 12 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
62
views
LEfSe
LEfSe
12 hours ago by
benkosta
• 0
0
votes
0
replies
52
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
10 hours ago by
Sara
▴ 30
1
vote
4
replies
325
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
10 hours ago by
hagl
▴ 10
0
votes
1
reply
94
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 13 hours ago by
Mohamed Abderrahmane
▴ 20 • written 14 hours ago by
matteo.levorato
• 0
0
votes
2
replies
104
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
13 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
103
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 15 hours ago by
i.sudbery
19k • written 16 hours ago by
DOBI
• 0
0
votes
0
replies
68
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
17 hours ago by
atharvakarkare14
▴ 10
5
votes
16
replies
563
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
17 hours ago by
Ruqaiya
• 0
0
votes
2
replies
137
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 hours ago by
Nafi
• 0
34
votes
22
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
5 hours ago by
noodle
▴ 570
0
votes
0
replies
60
views
Differential accessibility using DiffBinf
diffbind
18 hours ago by
Shloka
• 0
0
votes
0
replies
66
views
vg call vs vg surject
vg
variation
graphs
updated 12 hours ago by
GenoMax
141k • written 19 hours ago by
aliraza3119
• 0
0
votes
1
reply
96
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 12 hours ago by
GenoMax
141k • written 19 hours ago by
Winter
• 0
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 23 hours ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
173
views
Finding batch and outlayers
Pca
updated 15 hours ago by
christopher medway
▴ 450 • written 1 day ago by
Tigran
• 0
2
votes
2
replies
160
views
PDB related issue
rcsb
pdb
updated 1 day ago by
noodle
▴ 570 • written 1 day ago by
Nafi
• 0
0
votes
0
replies
87
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
15 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
308
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 10 hours ago by
dsull
★ 5.9k • written 1 day ago by
jinyu
▴ 10
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 18 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
417
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
1 day ago by
ashaneev07
▴ 20
0
votes
1
reply
136
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
726
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 1 day ago by
Francesco
▴ 10 • written 3.3 years ago by
gt
▴ 30
2
votes
2
replies
257
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 15 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
0
votes
0
replies
99
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 8 hours ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
255
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Francesco
▴ 10
116,668 results • Page
1 of 2334
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Comment: High Malat-1 expression in single cell data
Answer: Extract protein sequence
Answer: Extract protein sequence
C: How do I ask a question on Biostars?
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
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Recent Replies
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms: `…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
Hamtaro
▴ 50
Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
by
sansan_96
▴ 80
Hello, To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
Answer: Post-imputation plot
by
LChart
3.9k
The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
Comment: Differential Accessibility
by
Ram
43k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Extract protein sequence
by
anna
▴ 20
Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/ > so I want to understand how you reduced the 12063 genes to 978…
Comment: What should I consider as FASTA for dataset?
by
Nafi
• 0
Protein attribute prediction
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴ 40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴ 10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
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