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1,091 results • Page
1 of 22
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Rank
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Votes
Replies
4
votes
7
replies
423
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
just now by
e.r.zakiev
▴ 200
0
votes
0
replies
11
views
Synteny analysis
bacterial
synteny
genome
updated 16 minutes ago by
GenoMax
141k • written 18 minutes ago by
Namil
• 0
0
votes
1
reply
20
views
Genbank File Format
gbkformat
updated 26 minutes ago by
GenoMax
141k • written 35 minutes ago by
alenew.am
• 0
0
votes
3
replies
198
views
How should I make kallisto indexes?
kallisto
updated 36 minutes ago by
dsull
★ 5.9k • written 14 days ago by
bioinfo
▴ 150
0
votes
0
replies
21
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
59 minutes ago by
SSSJec
• 0
0
votes
2
replies
32
views
Software to separate reads from different individuals
software
development
nanopore
just now by
njornet
▴ 20
0
votes
0
replies
15
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
1 hour ago by
David
• 0
3
votes
5
replies
122
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
0
votes
1
reply
43
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
Mariana
▴ 10
0
votes
0
replies
18
views
metagenomic virome quality assessment
viromics
metagenomics
and
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
Petchimuthu
• 0
0
votes
2
replies
53
views
How to update R on ubuntu
installation
update
R
apt-get
1 hour ago by
Bosberg
▴ 50
3
votes
0
replies
39
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
3 hours ago by
Biostar
2.7k
0
votes
1
reply
69
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 hours ago by
GenoMax
141k • written 8 hours ago by
Ruqaiya
• 0
0
votes
1
reply
221
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
0
replies
40
views
LEfSe
LEfSe
3 hours ago by
benkosta
• 0
0
votes
0
replies
36
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
2 hours ago by
Sara
▴ 30
1
vote
4
replies
278
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
1 hour ago by
hagl
▴ 10
0
votes
1
reply
75
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 hours ago by
Mohamed Abderrahmane
▴ 20 • written 5 hours ago by
matteo.levorato
• 0
0
votes
2
replies
86
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
84
views
How to solve DESeq2 Error in checkFullRank(modelMatrix)?
RNA-Seq
DESeq2
updated 7 hours ago by
i.sudbery
19k • written 7 hours ago by
DOBI
• 0
0
votes
0
replies
51
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
8 hours ago by
atharvakarkare14
▴ 10
0
votes
2
replies
124
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 3 hours ago by
GenoMax
141k • written 10 hours ago by
WUSCHEL
▴ 750
5
votes
16
replies
543
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
8 hours ago by
Ruqaiya
• 0
0
votes
1
reply
77
views
What should I consider as FASTA for dataset?
PDB
FASTA
updated 3 hours ago by
GenoMax
141k • written 8 hours ago by
Nafi
• 0
34
votes
21
replies
1.5k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 4 hours ago by
i.sudbery
19k • written 1 day ago by
noodle
▴ 570
0
votes
0
replies
44
views
Differential accessibility using DiffBinf
diffbind
10 hours ago by
Shloka
• 0
0
votes
0
replies
48
views
vg call vs vg surject
vg
variation
graphs
updated 3 hours ago by
GenoMax
141k • written 10 hours ago by
aliraza3119
• 0
0
votes
1
reply
70
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 hours ago by
GenoMax
141k • written 11 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 15 hours ago by
Gordon Smyth
★ 7.0k • written 8 months ago by
Calum
▴ 10
0
votes
1
reply
155
views
Finding batch and outlayers
Pca
updated 6 hours ago by
christopher medway
▴ 450 • written 15 hours ago by
Tigran
• 0
2
votes
2
replies
145
views
PDB related issue
rcsb
pdb
updated 16 hours ago by
noodle
▴ 570 • written 19 hours ago by
Nafi
• 0
0
votes
0
replies
75
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
6 hours ago by
carlopecoraro2
★ 2.5k
0
votes
7
replies
273
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 2 hours ago by
dsull
★ 5.9k • written 21 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 10 hours ago by
Ram
43k • written 8 months ago by
Gio
• 0
2
votes
5
replies
399
views
Fetch table from clinvar database according to a list of rsid
python
clinvar
perl
21 hours ago by
ashaneev07
▴ 20
0
votes
1
reply
123
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
1
reply
714
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
242
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
0
votes
0
replies
87
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated just now by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
240
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 22 hours ago by
ATpoint
82k • written 1 day ago by
Francesco
▴ 10
0
votes
0
replies
111
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
127
views
Extract protein sequence
fasta
alighment
blast
1 day ago by
anna
▴ 20
0
votes
0
replies
116
views
Filter low express genes in microarray data
microarray
1 day ago by
Chris
▴ 260
0
votes
1
reply
303
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
315
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
310
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
339
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 19 hours ago by
Mensur Dlakic
★ 27k • written 2 days ago by
O.rka
▴ 710
0
votes
2
replies
239
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
204
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
1,091 results • Page
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Recent Votes
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
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
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Recent Replies
Answer: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Comment: Downsampling fastq file
by
Ram
43k
The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Ram
43k
Do the developers of toil mention biostars? Where do they direct their support requests to?
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
by
dsull
★ 5.9k
I recommend the ``kb ref`` method for two reasons: 1. The index created will yield more accurate mapping for datasets that have a substa…
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…
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