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182 results • Page
4 of 4
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0
votes
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148
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how to read graph_test output of monocle 3
monocle3
3 days ago by
synat.keam
▴ 100
0
votes
0
replies
150
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
3 days ago by
Emily
▴ 10
0
votes
0
replies
164
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
3 days ago by
avocado123
• 0
0
votes
2
replies
277
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
updated 3 days ago by
GenoMax
141k • written 4 days ago by
Begonia_pavonina
▴ 150
0
votes
1
reply
208
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 3 days ago by
ATpoint
82k • written 3 days ago by
AaronJaime
• 0
0
votes
0
replies
158
views
News:
Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis
Statistics
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
247
views
Annovar using R package
Annovar
gnomAD
R
3 days ago by
DKA
▴ 40
0
votes
0
replies
119
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
updated 3 days ago by
Ram
43k • written 4 days ago by
David Langenberger
11k
0
votes
0
replies
155
views
Designing single-stable RNA molecules
structure
RNA
3 days ago by
Edna
• 0
0
votes
0
replies
168
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
3 days ago by
simplitia
▴ 130
0
votes
2
replies
307
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
updated 3 days ago by
Ram
43k • written 4 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
11
replies
526
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
3 days ago by
atowns21
• 0
0
votes
0
replies
148
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
3 days ago by
turcoa1
• 0
0
votes
0
replies
190
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
3 days ago by
HarperReed
• 0
0
votes
7
replies
338
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
0
votes
0
replies
160
views
RNA-seq: full length gene
RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
Nargis
• 0
0
votes
3
replies
278
views
Highest variable features in single cell data
single-cell
updated 2 days ago by
bk11
★ 2.4k • written 4 days ago by
Kazo
▴ 10
0
votes
2
replies
257
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
The_PyPanda
▴ 10
0
votes
0
replies
165
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 2 days ago by
Ram
43k • written 3 days ago by
SineWave
• 0
0
votes
0
replies
489
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
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
0
votes
5
replies
333
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 1 day ago by
Istvan Albert
100k • written 5 days ago by
sehriban.buyukkilic
▴ 10
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
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
0
replies
113
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
0
replies
122
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
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
83
views
adjusting for confounders in LMER in R
confounders
LMER
R
1 day ago by
rene.j.erhardt
▴ 20
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
0
votes
1
reply
120
views
Downloading full alignments from Pfam
pfam
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
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
0
votes
0
replies
39
views
Differential accessibility using DiffBinf
diffbind
8 hours ago by
Shloka
• 0
182 results • Page
4 of 4
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
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.
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?
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