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325 results • Page
2 of 7
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
121
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
1 day ago by
Ali
• 0
2
votes
4
replies
256
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
0
votes
2
replies
193
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
1 day ago by
mropri
▴ 150
0
votes
1
reply
223
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 23 hours ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 1 day ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
564
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 500
2
votes
2
replies
198
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
bgbs
• 0
3
votes
7
replies
365
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
1 day ago by
ntsopoul
▴ 60
0
votes
0
replies
117
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
1 day ago by
shasabhi1
• 0
0
votes
0
replies
109
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
1 day ago by
Nishat
• 0
3
votes
3
replies
367
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
1 day ago by
ayushm64
• 0
0
votes
0
replies
120
views
what exactly is a k-mer table (remora)?
remora
basecall
1 day ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 1 day ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
330
views
Rename multiple fastq.gz files
fastq
next-gen
updated 1 day ago by
shenwei356
8.4k • written 2 days ago by
Jérémie
• 0
1
vote
1
reply
150
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
dsull
★ 5.8k • written 2 days ago by
niruf
• 0
0
votes
0
replies
143
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
225
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 2 days ago by
GenoMax
141k • written 2 days ago by
lorena9132
• 0
0
votes
0
replies
142
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
120
views
GWAS Phenotypes
GWAS
2 days ago by
solomoncharles77
▴ 90
4
votes
2
replies
226
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 2 days ago by
Ram
43k • written 2 days ago by
Adi
▴ 10
0
votes
2
replies
249
views
GSEA analysis in R
GSEA
R
Arabidopsis
7 hours ago by
Sudip
• 0
1
vote
2
replies
229
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 2 days ago by
Joe
21k • written 3 days ago by
ferdinand
▴ 10
0
votes
2
replies
333
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
1 day ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
335
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 2 days ago by
Ram
43k • written 2 days ago by
Spring
• 0
0
votes
0
replies
102
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
2 days ago by
QX
• 0
5
votes
4
replies
239
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
2 days ago by
Spring
• 0
2
votes
5
replies
326
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
1 day ago by
Bikram Kumar
• 0
1
vote
1
reply
272
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 2 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Milly
• 0
0
votes
1
reply
192
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 2 days ago by
ATpoint
81k • written 2 days ago by
Ravita
• 0
0
votes
2
replies
197
views
Getting marker genes for cell types
clustering
marker-genes
umap
2 days ago by
orzrzlyo
▴ 20
0
votes
1
reply
191
views
gene body coverage with RSeqQC
rna-seq
qc
updated 2 days ago by
BioinfGuru
★ 1.7k • written 2 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
219
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
David
• 0
0
votes
1
reply
171
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
393
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
225
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
166
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
312
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
182
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
159
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
232
views
RNAseq 1 control 2 different treatment
RNA-seq
2 days ago by
matteo.levorato
• 0
1
vote
0
replies
125
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Oscar
▴ 10
1
vote
2
replies
188
views
CombineGVCFs vs. MergeVcfs
CombineGVCFs
MergeVcfs
GATK
WGS
GVCF
updated 2 days ago by
Jeremy Leipzig
22k • written 3 days ago by
Sd
• 0
0
votes
0
replies
120
views
News:
Deadline Approaching: PETs for Public Health Challenge
privacy
public-health-challenge
updated 3 days ago by
Ram
43k • written 3 days ago by
polarise
▴ 380
0
votes
0
replies
128
views
How should I make kallisto indexes?
kallisto
updated 3 days ago by
GenoMax
141k • written 3 days ago by
bioinfo
▴ 150
1
vote
2
replies
178
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 3 days ago by
GenoMax
141k • written 3 days ago by
njornet
▴ 20
4
votes
0
replies
154
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
3 days ago by
Biostar
2.6k
2
votes
1
reply
211
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Manko47
• 0
4
votes
6
replies
375
views
Odd results with BLAST remote
blast
remote
NCBI
updated 2 days ago by
b.contreras.moreira
▴ 150 • written 3 days ago by
Begonia_pavonina
▴ 150
6
votes
8
replies
447
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 1 day ago by
dariober
14k • written 3 days ago by
manaswiniparija3
▴ 40
2
votes
0
replies
181
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by
Alexander
▴ 220
325 results • Page
2 of 7
Recent Votes
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
Answer: Problem with Mirdeep2 and Randfold output
Comment: Trying to write bwa mem -> samtools view -> samtools sort loop
C: Extract fasta sequences from a file using a list in another file.
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GenoMax
141k
Centurion
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jkbonfield
★ 1.2k
Popular Question
to
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▴ 250
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▴ 110
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Recent Replies
Answer: How to compare the quality of assemblies
by
shelkmike
★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou
by
nhaus
▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
bk11
★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output
by
otieno43
▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file
by
GenoMax
141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle
by
Ram
43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle
by
Joseph
• 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome
by
colindaven
6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Elisabeth Gasteiger
★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates
by
valentinatsar
• 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies
by
GenoMax
141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
Comment: Korean human genome reference file
by
GenoMax
141k
From NCBI: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_001712695.1/ Use the `Download` button or `curl/datasets`.
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