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500 results • Page
4 of 10
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
278
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
12 days ago by
bioinfo
▴ 150
0
votes
1
reply
200
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 13 days ago by
bk11
★ 2.4k • written 13 days ago by
sinhas
• 0
0
votes
1
reply
216
views
merging Seurat objects after SCT
Seurat
SCT
updated 13 days ago by
Ram
43k • written 13 days ago by
michelle.swarovski
• 0
0
votes
1
reply
218
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 13 days ago by
GenoMax
141k • written 13 days ago by
haiying.kong
▴ 360
0
votes
2
replies
275
views
RNAseq 1 control 2 different treatment
RNA-seq
13 days ago by
matteo.levorato
• 0
1
vote
0
replies
146
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 13 days ago by
Ram
43k • written 14 days ago by
Oscar
▴ 10
2
votes
0
replies
211
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
14 days ago by
Alexander
▴ 220
1
vote
1
reply
186
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 14 days ago by
GenoMax
141k • written 14 days ago by
eesiribloom
▴ 80
0
votes
0
replies
141
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
14 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
146
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
14 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
155
views
FreeBayes detection capacity
reads
freebayes
long
14 days ago by
quentinperriere
• 0
0
votes
2
replies
260
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
12 days ago by
DKA
▴ 40
0
votes
0
replies
166
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
14 days ago by
Hien
• 0
0
votes
2
replies
300
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
12 days ago by
Koketso
• 0
0
votes
0
replies
195
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 15 days ago by
Ram
43k • written 15 days ago by
menyawino
• 0
1
vote
3
replies
362
views
Ensembl gene id conversion
biomart
ensembl
updated 13 days ago by
ATpoint
82k • written 15 days ago by
naveedhasan2000
• 0
1
vote
2
replies
323
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 13 days ago by
Istvan Albert
100k • written 15 days ago by
Jiang
• 0
0
votes
0
replies
196
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
16 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
322
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
15 days ago by
O.rka
▴ 710
0
votes
6
replies
559
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
13 days ago by
Dunois
★ 2.5k
4
votes
7
replies
566
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 15 days ago by
Ram
43k • written 16 days ago by
AHerik
▴ 20
0
votes
0
replies
194
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 16 days ago by
Ram
43k • written 16 days ago by
roussine
▴ 10
0
votes
0
replies
184
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
17 days ago by
Ronin
• 0
4
votes
13
replies
889
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 12 days ago by
BioinfGuru
★ 1.7k • written 18 days ago by
matteo.levorato
• 0
2
votes
1
reply
251
views
VEP annotation --per_gene allele choice
VEP
updated 16 days ago by
Ram
43k • written 17 days ago by
atariw
▴ 10
0
votes
2
replies
293
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 16 days ago by
Zhenyu Zhang
★ 1.2k • written 17 days ago by
Apollonia
• 0
1
vote
1
reply
250
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 17 days ago by
Ram
43k • written 17 days ago by
Fish
• 0
0
votes
0
replies
187
views
Snakemake fails to find conda in PBS
snakemake
17 days ago by
yixinzeng
• 0
0
votes
0
replies
189
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
17 days ago by
Mary
• 0
0
votes
0
replies
182
views
Protein stability analysis
mutation
analysis
17 days ago by
marco.barr
▴ 80
1
vote
4
replies
399
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 16 days ago by
BioinfGuru
★ 1.7k • written 17 days ago by
Morteza
• 0
3
votes
1
reply
268
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 17 days ago by
Ram
43k • written 17 days ago by
rj.rezwan
• 0
0
votes
0
replies
172
views
Multiple Spike-Ins
MeRIP
Spike-In
17 days ago by
Adam
▴ 30
0
votes
0
replies
161
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 17 days ago by
Ram
43k • written 17 days ago by
Reno
• 0
2
votes
2
replies
278
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
161
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
18 days ago by
eesiribloom
▴ 80
0
votes
3
replies
326
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 16 days ago by
ATpoint
82k • written 18 days ago by
gdfsnkfns
• 0
0
votes
4
replies
326
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
17 days ago by
me
• 0
0
votes
2
replies
270
views
WGCNA
PCA
WGCNA
EIGENGENE
17 days ago by
rajasekargutha
▴ 60
0
votes
3
replies
273
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 17 days ago by
GenoMax
141k • written 18 days ago by
neish
• 0
1
vote
0
replies
159
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 18 days ago by
Ram
43k • written 18 days ago by
ian.will
▴ 30
0
votes
0
replies
108
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
18 days ago by
nhaus
▴ 310
1
vote
3
replies
288
views
True variants selection
vcf
bcftools
updated 17 days ago by
dthorbur
★ 1.9k • written 18 days ago by
maevalefeuvre
• 0
0
votes
1
reply
169
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 18 days ago by
Ram
43k • written 18 days ago by
CY
▴ 750
0
votes
0
replies
111
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
18 days ago by
JirMan
▴ 20
1
vote
1
reply
177
views
Failed to download data from EBI with ascp
EBI
aspera
updated 18 days ago by
GenoMax
141k • written 18 days ago by
biock
▴ 60
0
votes
0
replies
400
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
18 days ago by
Isaac
• 0
0
votes
0
replies
110
views
Combining VG graphs
vg
graphs
combine
18 days ago by
AshleeThomson
▴ 80
0
votes
0
replies
116
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 18 days ago by
Ram
43k • written 18 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
186
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 18 days ago by
Pierre Lindenbaum
161k • written 18 days ago by
Saran
▴ 50
500 results • Page
4 of 10
Recent Votes
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
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
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e.r.zakiev
▴ 200
Popular Question
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Bine
▴ 60
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★ 4.2k
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Recent Replies
Answer: metagenomic virome quality assessment
by
Mensur Dlakic
★ 27k
The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line? It is never a go…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
"I have seen other similar posts but a lot of the tools and websites suggested are down." Please show & share your research as part of you…
Comment: Software to separate reads from different individuals
by
njornet
▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf`, also observed an important issue of…
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…
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