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43 results • Page
1 of 1
Sort: Votes
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Views
Votes
Replies
34
votes
21
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 3 hours ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
5
votes
16
replies
535
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
7 hours ago by
Ruqaiya
• 0
3
votes
5
replies
104
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 1 hour ago by
dsull
★ 5.9k • written 4 hours ago by
Kazo
▴ 10
2
votes
2
replies
239
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 hours ago by
i.sudbery
19k • written 2 days ago by
vanbelj
▴ 40
2
votes
7
replies
1.2k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq
Salmon
Isoseq
updated 14 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
2
votes
11
replies
801
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 5 hours ago by
jkbonfield
★ 1.2k • written 12 days ago by
me
• 0
2
votes
5
replies
397
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
20 hours ago by
ashaneev07
▴ 20
2
votes
5
replies
316
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
8 hours ago by
analyst
▴ 30
2
votes
2
replies
143
views
PDB related issue
rcsb
pdb
updated 15 hours ago by
noodle
▴ 570 • written 18 hours ago by
Nafi
• 0
1
vote
6
replies
326
views
Downsampling fastq file
downsample
fastq
5 hours ago by
marco.barr
▴ 80
1
vote
0
replies
30
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
2 hours ago by
Biostar
2.7k
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 18 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 2 hours ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
1
vote
7
replies
423
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 24 minutes ago by
bk11
★ 2.4k • written 4 days ago by
starswillfade
▴ 10
1
vote
3
replies
238
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 21 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
1
vote
4
replies
270
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
1 hour ago by
hagl
▴ 10
1
vote
3
replies
332
views
PCA plot
DESeq2
PCAplot
updated 20 hours ago by
LauferVA
4.2k • written 4 days ago by
Aaliya
▴ 10
0
votes
7
replies
268
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 hour ago by
dsull
★ 5.9k • written 20 hours ago by
jinyu
▴ 10
0
votes
1
reply
32
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
Mariana
▴ 10
0
votes
2
replies
263
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
1 hour ago by
Fadi
• 0
0
votes
0
replies
13
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated 50 minutes ago by
GenoMax
141k • written 1 hour ago by
Petchimuthu
• 0
0
votes
0
replies
11
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
50 minutes ago by
David
• 0
0
votes
2
replies
42
views
How to update R on ubuntu
installation
update
R
apt-get
33 minutes ago by
Bosberg
▴ 50
0
votes
0
replies
11
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
18 minutes ago by
SSSJec
• 0
0
votes
1
reply
176
views
How should I make kallisto indexes?
kallisto
updated 9 minutes ago by
GenoMax
141k • written 14 days ago by
bioinfo
▴ 150
0
votes
1
reply
121
views
Downloading full alignments from Pfam
pfam
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
13
views
Software to separate reads from different individuals
software
development
nanopore
updated 6 minutes ago by
GenoMax
141k • written 21 minutes ago by
njornet
▴ 20
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 9 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
0
replies
41
views
Differential accessibility using DiffBinf
diffbind
9 hours ago by
Shloka
• 0
0
votes
0
replies
47
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
7 hours ago by
atharvakarkare14
▴ 10
0
votes
1
reply
81
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 6 hours ago by
i.sudbery
19k • written 7 hours ago by
DOBI
• 0
0
votes
1
reply
151
views
Finding batch and outlayers
Pca
updated 5 hours ago by
christopher medway
▴ 450 • written 15 hours ago by
Tigran
• 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
2
replies
82
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
4 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
68
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 4 hours ago by
Mohamed Abderrahmane
▴ 20 • written 4 hours ago by
matteo.levorato
• 0
0
votes
0
replies
36
views
LEfSe
LEfSe
3 hours ago by
benkosta
• 0
0
votes
1
reply
218
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 3 hours ago by
trausch
★ 1.9k • written 16 days ago by
zec018
• 0
0
votes
1
reply
60
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 2 hours ago by
GenoMax
141k • written 7 hours ago by
Ruqaiya
• 0
0
votes
2
replies
110
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
0
votes
1
reply
71
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 2 hours ago by
GenoMax
141k • written 8 hours ago by
Nafi
• 0
0
votes
0
replies
46
views
vg call vs vg surject
vg
variation
graphs
updated 2 hours ago by
GenoMax
141k • written 10 hours ago by
aliraza3119
• 0
0
votes
1
reply
63
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 2 hours ago by
GenoMax
141k • written 10 hours ago by
Winter
• 0
0
votes
0
replies
32
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
1 hour ago by
Sara
▴ 30
43 results • Page
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Recent Votes
Comment: NGS forensics: how to know if data is fabricated
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
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Recent Replies
Comment: Software to separate reads from different individuals
by
GenoMax
141k
Were these samples barcoded when they were run. If not then you won't be able to do much.
Comment: ScRNA data question
by
bk11
★ 2.4k
The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
Answer: How should I make kallisto indexes?
by
Bajaj
• 0
Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
Comment: How to update R on ubuntu
by
Bosberg
▴ 50
Thanks for the suggestion, but I get several lines of results (see below) and although there are directories called `"R"`, I can't find any…
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
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