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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
227
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 1 day ago by
Joe
21k • written 2 days ago by
ferdinand
▴ 10
0
votes
2
replies
326
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
10 hours ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
322
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 1 day ago by
Ram
43k • written 1 day ago by
Spring
• 0
0
votes
0
replies
97
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
1 day ago by
QX
• 0
5
votes
4
replies
235
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
1 day ago by
Spring
• 0
2
votes
5
replies
314
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
19 hours ago by
Bikram Kumar
• 0
1
vote
1
reply
266
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 1 day ago by
andres.firrincieli
3.6k • written 5 days ago by
Milly
• 0
0
votes
1
reply
191
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 1 day ago by
ATpoint
81k • written 1 day ago by
Ravita
• 0
0
votes
2
replies
190
views
Getting marker genes for cell types
clustering
marker-genes
umap
1 day ago by
orzrzlyo
▴ 20
0
votes
1
reply
187
views
gene body coverage with RSeqQC
rna-seq
qc
updated 1 day ago by
BioinfGuru
★ 1.7k • written 2 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
215
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 1 day ago by
Ram
43k • written 2 days ago by
David
• 0
0
votes
1
reply
167
views
Using adonis to include a random effect
mixed-model
adonis
updated 2 days ago by
LChart
3.9k • written 2 days ago by
leranwangcs
▴ 120
1
vote
3
replies
381
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 2 days ago by
LChart
3.9k • written 3 days ago by
leranwangcs
▴ 120
1
vote
2
replies
221
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
1
reply
158
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
sinhas
• 0
1
vote
5
replies
305
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
2 days ago by
shpak.max
▴ 50
0
votes
1
reply
179
views
merging Seurat objects after SCT
Seurat
SCT
updated 2 days ago by
Ram
43k • written 2 days ago by
michelle.swarovski
• 0
0
votes
1
reply
154
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 2 days ago by
GenoMax
141k • written 2 days ago by
haiying.kong
▴ 360
0
votes
2
replies
228
views
RNAseq 1 control 2 different treatment
RNA-seq
1 day ago by
matteo.levorato
• 0
1
vote
0
replies
114
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
1
vote
2
replies
181
views
CombineGVCFs vs. MergeVcfs
CombineGVCFs
MergeVcfs
GATK
WGS
GVCF
updated 1 day ago by
Jeremy Leipzig
22k • written 2 days ago by
Sd
• 0
0
votes
0
replies
111
views
News:
Deadline Approaching: PETs for Public Health Challenge
privacy
public-health-challenge
updated 2 days ago by
Ram
43k • written 2 days ago by
polarise
▴ 380
0
votes
0
replies
123
views
How should I make kallisto indexes?
kallisto
updated 2 days ago by
GenoMax
141k • written 2 days ago by
bioinfo
▴ 150
1
vote
2
replies
175
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
4
votes
0
replies
152
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
2 days ago by
Biostar
2.6k
2
votes
1
reply
208
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Manko47
• 0
4
votes
6
replies
367
views
Odd results with BLAST remote
blast
remote
NCBI
updated 1 day ago by
b.contreras.moreira
▴ 150 • written 2 days ago by
Begonia_pavonina
▴ 150
6
votes
8
replies
435
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 17 hours ago by
dariober
14k • written 2 days ago by
manaswiniparija3
▴ 40
2
votes
0
replies
168
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
2 days ago by
Alexander
▴ 220
1
vote
1
reply
149
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 2 days ago by
GenoMax
141k • written 2 days ago by
eesiribloom
▴ 80
0
votes
0
replies
109
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
2 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
112
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
2 days ago by
adarsh_pp
▴ 40
2
votes
4
replies
319
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 2 days ago by
GenoMax
141k • written 3 days ago by
Sony
▴ 10
0
votes
0
replies
125
views
FreeBayes detection capacity
reads
freebayes
long
2 days ago by
quentinperriere
• 0
0
votes
2
replies
197
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
15 hours ago by
DKA
▴ 40
0
votes
2
replies
224
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
2 days ago by
rj.rezwan
• 0
7
votes
7
replies
781
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 2 days ago by
Dunois
★ 2.5k • written 3 days ago by
AdviceSeeker
• 0
0
votes
0
replies
144
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
3 days ago by
Hien
• 0
0
votes
2
replies
253
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
1 day ago by
Koketso
• 0
1
vote
3
replies
383
views
Extracting data from a local NCBI taxonomy database
R
NCBI
xml
E-utilities
Blast
updated 3 days ago by
josev.die
▴ 60 • written 16 days ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
173
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 3 days ago by
Ram
43k • written 3 days ago by
menyawino
• 0
0
votes
0
replies
146
views
News:
Online course: Network Analysis in R
NetworkAnalyis
R
3 days ago by
carlopecoraro2
★ 2.5k
1
vote
3
replies
298
views
Ensembl gene id conversion
biomart
ensembl
updated 1 day ago by
ATpoint
81k • written 3 days ago by
naveedhasan2000
• 0
1
vote
2
replies
286
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 2 days ago by
Istvan Albert
100k • written 3 days ago by
Jiang
• 0
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 46 minutes ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
2
votes
3
replies
336
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 2 days ago by
ATpoint
81k • written 4 days ago by
IM
• 0
2
votes
1
reply
272
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene
genome
updated 4 days ago by
Alex Reynolds
35k • written 4 days ago by
natami
▴ 10
1
vote
1
reply
470
views
adding gene and CDS feature types in ensemble gtf annotation with transcript and exon features
GTF
GFF
transcript
CDS
exon
updated 4 days ago by
Pratik
★ 1.0k • written 4 days ago by
memy
▴ 20
0
votes
0
replies
186
views
Different flagstat number after using MergeBamAlignment
MergeBamAlignment
samtools
flagstat
4 days ago by
ThomasLam
• 0
3
votes
4
replies
346
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Sony
▴ 10
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
Answer: Pediococcus acidilactici sequence analysis
by
geneontologyhelp
▴ 340
If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
Answer: What is the normalization status of metabric data?
by
etiennedanis
▴ 10
I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
by
GenoMax
141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
Comment: How to reduce the variation of CIBERSORTx results?
by
LChart
3.9k
If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
Answer: Inconsistency in SNP detection pipelines for multi-sample analysis
by
LChart
3.9k
> To replicate GVCF behavior and avoid issues with 0/0 genotypes appearing as missing, I don't use the -v option I'm not sure what you m…
Comment: Supergnova stuck in tutorial
by
GenoMax
141k
Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
BioinfGuru
★ 1.7k
Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
Comment: Per base sequence content failed miserably
by
GenoMax
141k
What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
I guess the enlightening question is: duplicates of what?
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
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