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116,669 results • Page
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Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 hour ago by
Jacob
• 0
0
votes
3
replies
620
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 2 hours ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
113
views
Perfom a Gene Ontology Analysis from GO terms txt file
GO
RNASeq
updated 3 hours ago by
sansan_96
▴ 80 • written 4 hours ago by
Hamtaro
▴ 50
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
0
replies
39
views
Polishing genome assembly
polishing
Nanopore
PacBio
4 hours ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
85
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 5 hours ago by
LChart
3.9k • written 10 hours ago by
kl
▴ 10
0
votes
1
reply
77
views
Differential Accessibility
DiffBind
updated 5 hours ago by
Ram
43k • written 6 hours ago by
Shloka
• 0
0
votes
2
replies
97
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
20 minutes ago by
kim
• 0
3
votes
2
replies
245
views
Extract protein sequence
fasta
alignment
blast
5 hours ago by
anna
▴ 20
0
votes
3
replies
196
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 10 hours ago by
noodle
▴ 570 • written 21 hours ago by
WUSCHEL
▴ 750
0
votes
4
replies
184
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 7 hours ago by
Wayne
★ 2.0k • written 13 hours ago by
Mariana
▴ 10
0
votes
1
reply
82
views
metagenomic virome quality assessment
viromics
metagenomics
updated 9 hours ago by
Ram
43k • written 13 hours ago by
Petchimuthu
• 0
3
votes
7
replies
200
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
9 hours ago by
salias
• 0
0
votes
0
replies
50
views
Using limma in methylation EM-seq?
EM-seq
methylation
11 hours ago by
Lluís R.
★ 1.2k
4
votes
7
replies
490
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
10 hours ago by
e.r.zakiev
▴ 200
0
votes
0
replies
59
views
Synteny analysis
bacterial
synteny
genome
updated 11 hours ago by
GenoMax
141k • written 11 hours ago by
Namil
• 0
0
votes
2
replies
98
views
Genbank File Format
gbkformat
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 11 hours ago by
alenew.am
• 0
0
votes
5
replies
309
views
How should I make kallisto indexes?
kallisto
updated 9 hours ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
105
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
12 hours ago by
SSSJec
• 0
0
votes
3
replies
146
views
Software to separate reads from different individuals
software
development
nanopore
updated 7 hours ago by
GenoMax
141k • written 12 hours ago by
njornet
▴ 20
0
votes
0
replies
53
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
12 hours ago by
David
• 0
4
votes
5
replies
197
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 12 hours ago by
dsull
★ 5.9k • written 15 hours ago by
Kazo
▴ 10
0
votes
2
replies
114
views
How to update R on ubuntu
installation
update
R
apt-get
12 hours ago by
Bosberg
▴ 50
4
votes
0
replies
78
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
14 hours ago by
Biostar
2.7k
0
votes
1
reply
97
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 14 hours ago by
GenoMax
141k • written 19 hours ago by
Ruqaiya
• 0
0
votes
1
reply
248
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 15 hours ago by
trausch
★ 1.9k • written 17 days ago by
zec018
• 0
0
votes
0
replies
68
views
LEfSe
LEfSe
15 hours ago by
benkosta
• 0
0
votes
0
replies
57
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
13 hours ago by
Sara
▴ 30
1
vote
4
replies
328
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
13 hours ago by
hagl
▴ 10
0
votes
1
reply
99
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 16 hours ago by
Mohamed Abderrahmane
▴ 20 • written 16 hours ago by
matteo.levorato
• 0
0
votes
2
replies
109
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
16 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
107
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 18 hours ago by
i.sudbery
19k • written 19 hours ago by
DOBI
• 0
0
votes
0
replies
73
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
19 hours ago by
atharvakarkare14
▴ 10
5
votes
16
replies
569
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
19 hours ago by
Ruqaiya
• 0
0
votes
2
replies
146
views
What should I consider as FASTA for dataset?
PDB
FASTA
6 hours ago by
Nafi
• 0
34
votes
22
replies
1.6k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
8 hours ago by
noodle
▴ 570
0
votes
0
replies
64
views
Differential accessibility using DiffBinf
diffbind
21 hours ago by
Shloka
• 0
0
votes
0
replies
70
views
vg call vs vg surject
vg
variation
graphs
updated 14 hours ago by
GenoMax
141k • written 22 hours ago by
aliraza3119
• 0
0
votes
1
reply
100
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 14 hours ago by
GenoMax
141k • written 22 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 1 day ago by
Gordon Smyth
★ 7.1k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
176
views
Finding batch and outlayers
Pca
updated 17 hours ago by
christopher medway
▴ 450 • written 1 day ago by
Tigran
• 0
2
votes
2
replies
165
views
PDB related issue
rcsb
pdb
updated 1 day ago by
noodle
▴ 570 • written 1 day ago by
Nafi
• 0
0
votes
0
replies
90
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
17 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
311
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 13 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 21 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
420
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
139
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
729
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
260
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 18 hours ago by
i.sudbery
19k • written 3 days ago by
vanbelj
▴ 40
0
votes
0
replies
102
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 11 hours ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
116,669 results • Page
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The Biostar Herald for Monday, April 29, 2024
C: making a multi-fasta file out of 9 separate fasta file
Answer: Extract protein sequence
Answer: Having trouble using the create-profmark tool in the HMMER suite
Answer: GSEApy plot TypeError
Comment: High Malat-1 expression in single cell data
Answer: Extract protein sequence
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Comment: Landmark gene selection in L1000.
by
kim
• 0
thank you for reply, but i want some information for what microarray data are selected for L1000. thank you!
Answer: Why cd-hit-est not work when sequence identity threshold<0.95?
by
weidonglu
• 0
The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
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…
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