Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
38 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
1
view
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
just now by
David
• 0
3
votes
5
replies
74
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 8 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 18 minutes ago by
GenoMax
141k • written 40 minutes ago by
Mariana
▴ 10
0
votes
0
replies
11
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated just now by
GenoMax
141k • written 49 minutes ago by
Petchimuthu
• 0
0
votes
1
reply
24
views
How to update R on ubuntu
installation
update
R
apt-get
updated 30 minutes ago by
GenoMax
141k • written 55 minutes ago by
Bosberg
▴ 50
1
vote
0
replies
19
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
1 hour ago by
Biostar
2.7k
0
votes
1
reply
50
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 1 hour 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
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
40 minutes ago by
Sara
▴ 30
1
vote
4
replies
255
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
20 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 3 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
77
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
44
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
98
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
58
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
39
views
Differential accessibility using DiffBinf
diffbind
8 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 9 hours ago by
aliraza3119
• 0
0
votes
1
reply
52
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 1 hour 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
148
views
Finding batch and outlayers
Pca
updated 4 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
71
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
258
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 38 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
396
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 22 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
2
votes
2
replies
236
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
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
1
vote
3
replies
336
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
2
votes
5
replies
311
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
7 hours ago by
analyst
▴ 30
1
vote
3
replies
331
views
PCA plot
DESeq2
PCAplot
updated 19 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
1
vote
6
replies
323
views
Downsampling fastq file
downsample
fastq
4 hours ago by
marco.barr
▴ 80
2
votes
11
replies
800
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 4 hours ago by
jkbonfield
★ 1.2k • written 12 days ago by
me
• 0
0
votes
2
replies
261
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
19 minutes ago by
Fadi
• 0
38 results • Page
1 of 1
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
Recent Locations •
All
France,
1 minute ago
Zürich, Switzerland,
2 minutes ago
UCLA,
2 minutes ago
Italy,
3 minutes ago
United States,
3 minutes ago
London, United Kingdom,
4 minutes ago
Hong Kong,
5 minutes ago
Recent Awards •
All
Popular Question
to
Deepak Tanwar
★ 4.2k
Popular Question
to
Chris
▴ 260
Popular Question
to
Trivas
★ 1.7k
Popular Question
to
noodle
▴ 570
Popular Question
to
SaltedPork
▴ 170
Popular Question
to
christopher medway
▴ 450
Popular Question
to
Mohita
▴ 50
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.
Traffic: 2836 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6