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116,657 results • Page
1 of 2334
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Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
10 minutes ago by
David
• 0
3
votes
5
replies
77
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 18 minutes ago by
dsull
★ 5.9k • written 3 hours ago by
Kazo
▴ 10
0
votes
1
reply
22
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 28 minutes ago by
GenoMax
141k • written 50 minutes ago by
Mariana
▴ 10
0
votes
0
replies
11
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated 10 minutes ago by
GenoMax
141k • written 1 hour ago by
Petchimuthu
• 0
0
votes
1
reply
26
views
How to update R on ubuntu
installation
update
R
apt-get
updated 49 minutes ago by
GenoMax
141k • written 1 hour ago by
Bosberg
▴ 50
1
vote
0
replies
21
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
1 hour ago by
Biostar
2.7k
0
votes
1
reply
54
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
Ruqaiya
• 0
0
votes
1
reply
212
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 2 hours ago by
trausch
★ 1.9k • written 16 days ago by
zec018
• 0
0
votes
0
replies
26
views
LEfSe
LEfSe
2 hours ago by
benkosta
• 0
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
24
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
50 minutes ago by
Sara
▴ 30
1
vote
4
replies
257
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
30 minutes ago by
hagl
▴ 10
0
votes
1
reply
59
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 3 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 hours ago by
matteo.levorato
• 0
0
votes
2
replies
76
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
78
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 5 hours ago by
i.sudbery
19k • written 6 hours ago by
DOBI
• 0
0
votes
0
replies
45
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
6 hours ago by
atharvakarkare14
▴ 10
0
votes
2
replies
100
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 hours ago by
GenoMax
141k • written 9 hours ago by
WUSCHEL
▴ 750
5
votes
16
replies
532
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
7 hours ago by
Ruqaiya
• 0
0
votes
1
reply
60
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 2 hours ago by
GenoMax
141k • written 7 hours ago by
Nafi
• 0
33
votes
21
replies
1.4k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 2 hours ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
0
votes
0
replies
40
views
Differential accessibility using DiffBinf
diffbind
8 hours ago by
Shloka
• 0
0
votes
0
replies
44
views
vg call vs vg surject
vg
variation
graphs
updated 2 hours ago by
GenoMax
141k • written 9 hours ago by
aliraza3119
• 0
0
votes
1
reply
55
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 hours ago by
GenoMax
141k • written 9 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 13 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
149
views
Finding batch and outlayers
Pca
updated 5 hours ago by
christopher medway
▴ 450 • written 14 hours ago by
Tigran
• 0
2
votes
2
replies
142
views
PDB related issue
rcsb
pdb
updated 14 hours ago by
noodle
▴ 570 • written 17 hours ago by
Nafi
• 0
0
votes
0
replies
72
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
5 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
262
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 51 minutes ago by
dsull
★ 5.9k • written 19 hours 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 8 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
397
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
19 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
121
views
Downloading full alignments from Pfam
pfam
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
711
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
237
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 hours ago by
i.sudbery
19k • written 2 days ago by
vanbelj
▴ 40
0
votes
0
replies
84
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
237
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 20 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
108
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
1 day ago by
tnminh89
▴ 10
0
votes
0
replies
123
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
114
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
300
views
absolute path for symbolic links in Snakefile
Snakemake
updated 1 day ago by
Jesse
▴ 740 • written 9 days ago by
yifangt86
▴ 60
0
votes
2
replies
312
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 1 day ago by
Jesse
▴ 740 • written 4 days ago by
Broccoli
• 0
2
votes
3
replies
306
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 1 day ago by
Arup Ghosh
3.2k • written 2 days ago by
chaco001
▴ 40
1
vote
3
replies
337
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 17 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
0
votes
2
replies
237
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
2 days ago by
Guille
• 0
2
votes
1
reply
201
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
pairedttest
▴ 10
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 2 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
0
votes
0
replies
491
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
2 days ago by
biocellbio
• 0
4
votes
8
replies
585
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 2 days ago by
Alex Reynolds
35k • written 3 days ago by
J
▴ 10
4
votes
7
replies
638
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 2 days ago by
dsull
★ 5.9k • written 6 days ago by
qudrat.nii
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 2 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
2
replies
300
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 3 days ago by
dsull
★ 5.9k • written 3 days ago by
Aaliya
▴ 10
116,657 results • Page
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Recent Votes
Answer: High Malat-1 expression in single cell data
Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
A: Bam And Indexed Bam Files
High Malat-1 expression in single cell data
Segmentation fault using gemma
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Fadi
• 0
Where can I ask this question? Apparently this the place where you can help for toil?
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Dear Gordon, excuse me for not being specific regarding your advice. What would be the best way if I wanted to add new annotations to the …
Comment: Programmatically retrieving positions of protein active site residues
by
GenoMax
141k
While you wait to get answers, consider asking ChatGPT for a solution. You may be pleasantly surprised with pointers/code you will get.
Comment: High Malat-1 expression in single cell data
by
Kazo
▴ 10
When I perform differential analysis, the genes that could be considered as markers in this malat1 high cluster tend to be nuclear genes. D…
Comment: How to update R on ubuntu
by
GenoMax
141k
You can check where the application was installed using: https://unix.stackexchange.com/questions/39590/apt-get-install-where-does-it-go T…
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
"using RNA-seq for allele imbalanced gene expression" -> Not sure what you mean by that; thousands of studies (including some ongoing studi…
Comment: High Malat-1 expression in single cell data
by
Kazo
▴ 10
I have noticed in articles that people define low-quality clusters and remove them from the data, but they don't exactly explain what makes…
Answer: High Malat-1 expression in single cell data
by
dsull
★ 5.9k
I'm assuming you read https://kb.10xgenomics.com/hc/en-us/articles/360004729092-Why-do-I-see-high-levels-of-Malat1-in-my-gene-expression-da…
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
I actually advised you not to remove duplicate probes, especially as you seem to be use probe annotation that is very old and possibly out …
Comment: Segmentation fault using gemma
by
dimpleadiwal050896
• 0
Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
Comment: Can I merge Hi-C fastq files from different lanes?
by
GenoMax
141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset?
by
GenoMax
141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository?
by
GenoMax
141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2
by
GenoMax
141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
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