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121,274 results • Page
1 of 2426
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0
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Decision making on choosing the based on tblastn result
interpretation
tblastn
BLAST
E-score
updated 50 minutes ago by
GenoMax
151k • written 1 hour ago by
srestha
• 0
7
votes
7
replies
2.8k
views
How to Identify the pathogenicity of a set of variants (by using ACMG guidelines)?
pathogenicity
SNP
variants
updated 18 hours ago by
Damianos P. Melidis
▴ 40 • written 6.5 years ago by
DanielC
▴ 190
0
votes
2
replies
202
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard
bwa
1 day ago by
curious
▴ 890
0
votes
0
replies
103
views
use AverageExpression to stratify samples
scRNA
1 day ago by
ndra1456
• 0
837
votes
170
replies
178k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
0
replies
91
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
1 day ago by
Wenhai
• 0
0
votes
0
replies
401
views
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clustering at 97%)
vsearch
updated 1 day ago by
GenoMax
151k • written 1 day ago by
salma.sarker
• 0
0
votes
0
replies
110
views
RepeatMasker output file question
RepeatMasker
1 day ago by
xinguok794
• 0
1
vote
1
reply
385
views
Which GWAS tool to use that can work on Czech cases and British controls, on a binary trait?
plink2
gwas
saige
updated 1 day ago by
LChart
4.9k • written 3 days ago by
anita.szabo08
▴ 10
0
votes
2
replies
219
views
Unsure whether or not I overcorrected for batch effect in dataset
Quality
Plot
PCA
Control
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Megan
▴ 50
0
votes
3
replies
213
views
Primer removal in amplicon sequencing
removal
Primer
Amplicon
DADA2
sequencing
updated 1 day ago by
GenoMax
151k • written 1 day ago by
sxf520
• 0
0
votes
1
reply
214
views
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
GATK
VCF
BSQR
updated 2 days ago by
Ram
45k • written 2 days ago by
iamsmor
• 0
0
votes
1
reply
197
views
Batch correction without biological covariates
Combat-seq
RNA-seq
batch-correction
updated 2 days ago by
Ram
45k • written 2 days ago by
as823jk
• 0
0
votes
1
reply
170
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 2 days ago by
Ram
45k • written 2 days ago by
bioinfo
▴ 160
1
vote
3
replies
244
views
RagTag results
NGS
scaffolding
RagTag
gaps
updated 2 days ago by
shelkmike
★ 1.6k • written 2 days ago by
synthiiihuh
• 0
0
votes
1
reply
202
views
Tools that output positions of matching kmers
sequences
genomics
kmers
updated 2 days ago by
GenoMax
151k • written 2 days ago by
gil.hornung
▴ 100
2
votes
4
replies
306
views
mitochondrial assamply use NOVOplasty
mitochondrial
genome
mammles
updated 2 days ago by
cfos4698
★ 1.1k • written 3 days ago by
m90
▴ 30
0
votes
2
replies
220
views
Still bad phred score after fastp
phred
fastp
updated 2 days ago by
Ram
45k • written 2 days ago by
Shazel
• 0
0
votes
1
reply
187
views
Cytohubba problem and difference networks
Network
cytoscape
cytohubba
analysis
updated 2 days ago by
Scooter
▴ 310 • written 3 days ago by
mastorehpournazari
• 0
0
votes
1
reply
378
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
updated 2 days ago by
Scooter
▴ 310 • written 25 days ago by
Adrian
• 0
3
votes
1
reply
186
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 2 days ago by
GenoMax
151k • written 3 days ago by
biostars
▴ 30
2
votes
4
replies
322
views
Mass-spectrometry proteomics
Proteomics
analysis
updated 1 day ago by
Gordon Smyth
★ 8.1k • written 3 days ago by
Nasim Gandomdoust
• 0
7
votes
3
replies
315
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome
QC
velocity
single-cell
intron
updated 2 days ago by
jared.andrews07
★ 18k • written 3 days ago by
txema.heredia
▴ 240
0
votes
0
replies
136
views
News:
Eukaryotic eDNA Metabarcoding Course (14–18 July, Online)
Metabarcoding
eDNA
Genomics
Nanopore
3 days ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
315
views
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
macs2
cutandrun
chipseq
updated 2 days ago by
ATpoint
88k • written 3 days ago by
sk
• 0
7
votes
12
replies
651
views
miRNA low mapping(Qiagen miRNA Library Prep)
Qiagen
pipeline
trimming
alignment
miRNA
updated 3 days ago by
GenoMax
151k • written 6 days ago by
anthony.santana.703.j
▴ 10
0
votes
12
replies
938
views
STAR alignment not detecting some transcripts / custom reference
star
bwa
rna-seq
alignment
scrna-seq
updated 2 days ago by
rfran010
★ 1.5k • written 8 days ago by
npont
• 0
0
votes
0
replies
144
views
eHOMD database: Ref seq Aligned FASTA vs Full RefSeq?
HOMD
database
3 days ago by
bioinfo
▴ 60
2
votes
3
replies
392
views
pysam header and body
bam
pysam
view
updated 3 days ago by
dariober
15k • written 5 days ago by
Matteo Ungaro
▴ 120
3
votes
1
reply
301
views
Discrepency in assembly sizes
Pacbio
assembly
Kmer
updated 3 days ago by
shelkmike
★ 1.6k • written 5 days ago by
hpapoli
▴ 170
0
votes
1
reply
192
views
fasterq-dump fails before completing lookup
lookup
incomplete
fasterq-dump
updated 3 days ago by
GenoMax
151k • written 3 days ago by
nmannda148
• 0
4
votes
1
reply
230
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
3 days ago by
anna
▴ 40
0
votes
4
replies
358
views
ATACSEQ normlization for bigwig files
normalization
atac-seq
updated 4 days ago by
ATpoint
88k • written 4 days ago by
RD
▴ 20
4
votes
6
replies
461
views
finding gene sequence from WGS data
gene
WGS
updated 2 days ago by
swbarnes2
15k • written 4 days ago by
analyst
▴ 70
0
votes
0
replies
173
views
Question about Protein-protein-DNA complex prediction
prediction
protein
4 days ago by
mickley413
• 0
1
vote
10
replies
2.1k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 4 days ago by
s.faria
• 0 • written 2.7 years ago by
Gerard
▴ 10
2
votes
4
replies
636
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis
method
rnaseq
updated 4 days ago by
mbyvcm
▴ 460 • written 9 days ago by
cgibbsm
▴ 20
1
vote
2
replies
298
views
pddg+odgi+vg to perform pangenome analysis to cyanobacteria
odgi
pggb
help
pangenome
vg
updated 4 days ago by
GenoMax
151k • written 4 days ago by
snmdba
▴ 10
1
vote
2
replies
299
views
Comparing sets of genes for similarity
R
jaccard
genes
marker
clustering
2 days ago by
yura.grabovska
▴ 780
0
votes
0
replies
201
views
News:
Network Analysis in Systems Biology - 2 seats left
Bioconductor
SystemsBiology
R
NetworkAnalysis
RNAseq
4 days ago by
Physalia-courses
★ 2.6k
2
votes
5
replies
442
views
Running Unicycler with a merged fastq file
unicycler
bacterial-genome
assembly
updated 3 days ago by
GenoMax
151k • written 4 days ago by
Assa Yeroslaviz
★ 1.9k
3
votes
5
replies
494
views
Assemblers for short read bacterial isolates data
data
isolates
assembly
shotgun
updated 1 day ago by
Mensur Dlakic
★ 29k • written 6 days ago by
shevch2009
▴ 20
0
votes
2
replies
329
views
Biopython get_terminals() doesn't get all terminals
biopython
tree
get_terminals
gtdb
5 days ago by
khp35
• 0
0
votes
0
replies
214
views
Covariate Selection for DESeq2/ANCOM-BC: Alpha vs. Beta Diversity Findings
ANCOM-BC
microbiome
covariates
DESeq2
PERMANOVA
5 days ago by
bioinfo
▴ 60
0
votes
1
reply
304
views
NF core rna-seq pipeline
nf-core
nextflow
pipeline
rnaseq
updated 5 days ago by
GenoMax
151k • written 5 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
221
views
Need Access to RadGraph2 Dataset from PhysioNet — Stuck at CITI Course Step
dataset
5 days ago by
z.mohammadi64
• 0
6
votes
3
replies
368
views
Both up- and down-regulated gene sets return the same GO pathway analysis results?
DEseq2
GO-analysis
3 days ago by
xqyn
▴ 60
0
votes
1
reply
273
views
Discrepancies calculatin average coverage with Bedtools and Mosdepth
mosdepth
human
bedtools
libraries
illumina
updated 5 days ago by
Pierre Lindenbaum
166k • written 5 days ago by
María José
▴ 10
4
votes
7
replies
3.7k
views
Michigan imputation server error
TOPMed
VCF
updated 5 days ago by
Joel Wallenius
▴ 220 • written 4.9 years ago by
AR
• 0
2
votes
8
replies
717
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant
Somatic_data
Help
Copy
2 days ago by
AIMAR
▴ 10
121,274 results • Page
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Recent Votes
C: Somatic vs Germline Variant Calling
Somatic vs Germline Variant Calling
Somatic vs Germline Variant Calling
MAF (minor allele frequency) calculation for finding rare variants from TCGA
MAF (minor allele frequency) calculation for finding rare variants from TCGA
Comment: What is gnomAD allele frequency
Comment: What is gnomAD allele frequency
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Recent Replies
Comment: Decision making on choosing the based on tblastn result
by
GenoMax
151k
What is your aim here? Asking the right question will ensure that you get the correct answer. Query coverage is important. Other hits may …
Comment: VCF2MAF structural variant file issue.
by
eebloom
▴ 90
I have the same issue, did you find a solution?
Comment: de novo chromosome level assembly
by
colindaven
7.5k
Look at Ragtag on github, assuming you have a close reference to align against. Else your main option is spending more on Hi-C data. Else m…
Comment: Currently recommended Oxford Nanopore data basecalling and preprocessing pipelin
by
Asan Emirsale
• 0
the `dorado` does remove adapters for only 10.4.1 etc data. If you have data from r9.4.1, you should activate `---trim` flag. I suggest al…
Comment: de novo chromosome level assembly
by
mthm
▴ 80
I suppose the first one, since I don't have the information of the real chromosome
Answer: How to Identify the pathogenicity of a set of variants (by using ACMG guidelines
by
Damianos P. Melidis
▴ 40
Dear DK, Don't know if you are still interested in bioinformatics tools to implement ACMG but if you do let me share this biostars [post…
Comment: ACMG assignment tools
by
Damianos P. Melidis
▴ 40
Hey, just to update with more tools: - the wonderful* [TAPES][1] - [vaRHC][2] - [auto-acmg][3] - genotoscope (see mark at the end) Please…
Comment: Mass-spectrometry proteomics
by
Gordon Smyth
★ 8.1k
limpa shares the full capabilities of the limma package, which includes adjustment for batch effects and outliers. To adjust for batch effe…
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
curious
▴ 890
There are no secondary alignments as per : samtools -f 0x100 {my_bam} I only get secondary alignments if I add the `-a` flag to bwa …
Comment: Assemblers for short read bacterial isolates data
by
Mensur Dlakic
★ 29k
Binning can be done in seconds, and there is no harm in trying it. If you run CheckM analyses before and after binning, it should give you …
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
GenoMax
151k
Can you provide the actual metrics output? > What could be causing this? Perhaps your data has no secondary/supplementary alignments. Al…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
Megan
▴ 50
Thank you so much for the suggestion. I have included my code in the post.
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
`DADA2` pipeline states that all non-biological nucleotides need to be removed so choose accordingly: https://benjjneb.github.io/dada2/tuto…
Comment: Mass-spectrometry proteomics
by
Nasim Gandomdoust
• 0
Thank you for your reply. I would like to know if the package can handle batch effects and outlier samples too.
Answer: Which GWAS tool to use that can work on Czech cases and British controls, on a b
by
LChart
4.9k
There is really no way for you to do this analysis - having cases and controls perfectly confounded by populations means that every variant…
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