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116,656 results • Page
1 of 2334
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3
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4
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49
views
High Malat-1 expression in single cell data
cell
analysis
single
just now by
Kazo
▴ 10
0
votes
0
replies
1
view
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
just now by
Mariana
▴ 10
0
votes
0
replies
7
views
metagenomic virome quality assessment
viromics
metagenomics
and
10 minutes ago by
Petchimuthu
• 0
0
votes
1
reply
14
views
How to update R on ubuntu
installation
update
R
apt-get
updated just now by
GenoMax
141k • written 25 minutes ago by
Bosberg
▴ 50
1
vote
0
replies
14
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
53 minutes ago by
Biostar
2.7k
0
votes
1
reply
48
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 1 hour ago by
GenoMax
141k • written 5 hours ago by
Ruqaiya
• 0
0
votes
1
reply
206
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 1 hour ago by
trausch
★ 1.9k • written 16 days ago by
zec018
• 0
0
votes
0
replies
21
views
LEfSe
LEfSe
1 hour 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
20
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
just now by
Sara
▴ 30
1
vote
3
replies
236
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 27 minutes ago by
Gordon Smyth
★ 7.0k • written 2 days ago by
hagl
▴ 10
0
votes
1
reply
52
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 3 hours ago by
Mohamed Abderrahmane
▴ 20 • written 3 hours ago by
matteo.levorato
• 0
0
votes
2
replies
67
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
77
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 4 hours ago by
i.sudbery
19k • written 5 hours ago by
DOBI
• 0
0
votes
0
replies
39
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
95
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 1 hour ago by
GenoMax
141k • written 8 hours ago by
WUSCHEL
▴ 750
5
votes
16
replies
531
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
6 hours ago by
Ruqaiya
• 0
0
votes
1
reply
56
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 1 hour ago by
GenoMax
141k • written 6 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
38
views
Differential accessibility using DiffBinf
diffbind
7 hours ago by
Shloka
• 0
0
votes
0
replies
43
views
vg call vs vg surject
vg
variation
graphs
updated 1 hour ago by
GenoMax
141k • written 8 hours ago by
aliraza3119
• 0
0
votes
1
reply
51
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 1 hour ago by
GenoMax
141k • written 8 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 12 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
141
views
Finding batch and outlayers
Pca
updated 4 hours ago by
christopher medway
▴ 450 • written 13 hours ago by
Tigran
• 0
2
votes
2
replies
142
views
PDB related issue
rcsb
pdb
updated 13 hours ago by
noodle
▴ 570 • written 17 hours ago by
Nafi
• 0
0
votes
0
replies
71
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
245
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated just now 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 7 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
395
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
120
views
Downloading full alignments from Pfam
pfam
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
709
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
236
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 4 hours ago by
i.sudbery
19k • written 2 days ago by
vanbelj
▴ 40
0
votes
0
replies
83
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 19 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
107
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
122
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
113
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
305
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
335
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
236
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
200
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
488
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
584
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
635
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
297
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
3
votes
0
replies
188
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 2 days ago by
Ram
43k • written 3 days ago by
Claire Watson
▴ 60
116,656 results • Page
1 of 2334
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Answer: High Malat-1 expression in single cell data
The Biostar Herald for Monday, April 29, 2024
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High Malat-1 expression in single cell data
Segmentation fault using gemma
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Recent Replies
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.
Answer: High Malat-1 expression in single cell data
by
ATpoint
82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
by
trausch
★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Thats very intersting! What are the features in your classifier?
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
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