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121,269 results • Page
1 of 2426
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0
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6
views
RepeatMasker output file question
RepeatMasker
16 minutes ago by
xinguok794
• 0
1
vote
1
reply
294
views
Which GWAS tool to use that can work on Czech cases and British controls, on a binary trait?
plink2
gwas
saige
updated 3 hours ago by
LChart
4.9k • written 1 day ago by
anita.szabo08
▴ 10
0
votes
1
reply
58
views
Unsure whether or not I overcorrected for batch effect in dataset
Quality
Plot
Control
PCA
updated 4 hours ago by
cfos4698
★ 1.1k • written 5 hours ago by
Megan
▴ 50
0
votes
2
replies
68
views
Primer removal in amplicon sequencing
removal
Primer
Amplicon
DADA2
sequencing
7 hours ago by
sxf520
• 0
0
votes
1
reply
118
views
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
GATK
VCF
BSQR
updated 9 hours ago by
Ram
45k • written 10 hours ago by
iamsmor
• 0
0
votes
1
reply
113
views
Batch correction without biological covariates
Combat-seq
RNA-seq
batch-correction
updated 9 hours ago by
Ram
45k • written 17 hours ago by
as823jk
• 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
1
reply
95
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 9 hours ago by
Ram
45k • written 14 hours ago by
bioinfo
▴ 160
1
vote
3
replies
168
views
RagTag results
NGS
scaffolding
RagTag
gaps
updated 20 hours ago by
shelkmike
★ 1.6k • written 23 hours ago by
synthiiihuh
• 0
0
votes
1
reply
129
views
Tools that output positions of matching kmers
sequences
genomics
kmers
updated 19 hours ago by
GenoMax
151k • written 1 day ago by
gil.hornung
▴ 100
2
votes
4
replies
232
views
mitochondrial assamply use NOVOplasty
mitochondrial
genome
mammles
updated 1 day ago by
cfos4698
★ 1.1k • written 1 day ago by
m90
▴ 30
0
votes
2
replies
147
views
Still bad phred score after fastp
phred
fastp
updated 9 hours ago by
Ram
45k • written 1 day ago by
Shazel
• 0
0
votes
1
reply
133
views
Cytohubba problem and difference networks
Network
cytoscape
cytohubba
analysis
updated 1 day ago by
Scooter
▴ 310 • written 1 day ago by
mastorehpournazari
• 0
0
votes
1
reply
325
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
updated 1 day ago by
Scooter
▴ 310 • written 23 days ago by
Adrian
• 0
3
votes
1
reply
129
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 19 hours ago by
GenoMax
151k • written 1 day ago by
biostars
▴ 30
0
votes
2
replies
163
views
Mass-spectrometry proteomics
Proteomics
analysis
updated 23 hours ago by
Gordon Smyth
★ 8.1k • written 1 day ago by
Nasim Gandomdoust
• 0
7
votes
3
replies
225
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome
QC
velocity
single-cell
intron
updated 16 hours ago by
jared.andrews07
★ 18k • written 1 day ago by
txema.heredia
▴ 240
0
votes
0
replies
89
views
News:
Eukaryotic eDNA Metabarcoding Course (14–18 July, Online)
Metabarcoding
eDNA
Genomics
Nanopore
1 day ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
249
views
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
macs2
cutandrun
chipseq
updated 1 day ago by
ATpoint
88k • written 2 days ago by
sk
• 0
6
votes
12
replies
548
views
miRNA low mapping(Qiagen miRNA Library Prep)
Qiagen
pipeline
trimming
alignment
miRNA
updated 1 day ago by
GenoMax
151k • written 4 days ago by
anthony.santana.703.j
• 0
0
votes
12
replies
843
views
STAR alignment not detecting some transcripts / custom reference
star
bwa
rna-seq
alignment
scrna-seq
updated 23 hours ago by
rfran010
★ 1.5k • written 6 days ago by
npont
• 0
0
votes
0
replies
94
views
eHOMD database: Ref seq Aligned FASTA vs Full RefSeq?
HOMD
database
1 day ago by
bioinfo
▴ 60
2
votes
3
replies
326
views
pysam header and body
bam
pysam
view
updated 1 day ago by
dariober
15k • written 3 days ago by
Matteo Ungaro
▴ 120
3
votes
1
reply
241
views
Discrepency in assembly sizes
Pacbio
assembly
Kmer
updated 2 days ago by
shelkmike
★ 1.6k • written 3 days ago by
hpapoli
▴ 170
0
votes
1
reply
138
views
fasterq-dump fails before completing lookup
lookup
incomplete
fasterq-dump
updated 1 day ago by
GenoMax
151k • written 2 days ago by
nmannda148
• 0
4
votes
1
reply
176
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
1 day ago by
anna
▴ 40
0
votes
4
replies
281
views
ATACSEQ normlization for bigwig files
normalization
atac-seq
updated 2 days ago by
ATpoint
88k • written 2 days ago by
RD
▴ 20
4
votes
6
replies
369
views
finding gene sequence from WGS data
gene
WGS
updated 11 hours ago by
swbarnes2
15k • written 2 days ago by
analyst
▴ 70
0
votes
0
replies
123
views
Question about Protein-protein-DNA complex prediction
prediction
protein
2 days ago by
mickley413
• 0
1
vote
10
replies
2.0k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 2 days ago by
s.faria
• 0 • written 2.7 years ago by
Gerard
▴ 10
2
votes
4
replies
578
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis
method
rnaseq
updated 2 days ago by
mbyvcm
▴ 460 • written 8 days ago by
cgibbsm
▴ 20
1
vote
2
replies
235
views
pddg+odgi+vg to perform pangenome analysis to cyanobacteria
odgi
pggb
help
pangenome
vg
updated 2 days ago by
GenoMax
151k • written 2 days ago by
snmdba
▴ 10
1
vote
2
replies
235
views
Comparing sets of genes for similarity
R
jaccard
genes
marker
clustering
22 hours ago by
yura.grabovska
▴ 780
0
votes
0
replies
149
views
News:
Network Analysis in Systems Biology - 2 seats left
Bioconductor
SystemsBiology
R
NetworkAnalysis
RNAseq
2 days ago by
Physalia-courses
★ 2.6k
2
votes
5
replies
365
views
Running Unicycler with a merged fastq file
unicycler
bacterial-genome
assembly
updated 1 day ago by
GenoMax
151k • written 3 days ago by
Assa Yeroslaviz
★ 1.9k
2
votes
4
replies
387
views
Assemblers for short read bacterial isolates data
data
isolates
assembly
shotgun
2 days ago by
shevch2009
▴ 20
0
votes
2
replies
271
views
Biopython get_terminals() doesn't get all terminals
biopython
tree
get_terminals
gtdb
3 days ago by
khp35
• 0
0
votes
0
replies
162
views
Covariate Selection for DESeq2/ANCOM-BC: Alpha vs. Beta Diversity Findings
ANCOM-BC
microbiome
covariates
DESeq2
PERMANOVA
3 days ago by
bioinfo
▴ 60
0
votes
1
reply
246
views
NF core rna-seq pipeline
nf-core
nextflow
pipeline
rnaseq
updated 3 days ago by
GenoMax
151k • written 3 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
166
views
Need Access to RadGraph2 Dataset from PhysioNet — Stuck at CITI Course Step
dataset
3 days ago by
z.mohammadi64
• 0
6
votes
3
replies
312
views
Both up- and down-regulated gene sets return the same GO pathway analysis results?
DEseq2
GO-analysis
1 day ago by
xqyn
▴ 60
0
votes
1
reply
219
views
Discrepancies calculatin average coverage with Bedtools and Mosdepth
mosdepth
human
bedtools
libraries
illumina
updated 3 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
María José
▴ 10
4
votes
7
replies
3.6k
views
Michigan imputation server error
TOPMed
VCF
updated 3 days ago by
Joel Wallenius
▴ 220 • written 4.9 years ago by
AR
• 0
2
votes
8
replies
629
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant
Somatic_data
Help
Copy
23 hours ago by
AIMAR
▴ 10
2
votes
2
replies
275
views
Error with bigWigAverageOverBed
usc
human
libraries
illumina
bigWigAverageOverBed
updated 3 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
María José
▴ 10
8
votes
11
replies
582
views
de novo chromosome level assembly
genome
assembly
chromsome
updated 1 day ago by
lieven.sterck
15k • written 4 days ago by
mthm
▴ 80
6
votes
2
replies
323
views
How is PLINK obtaining p-values and coefficients for linear regression
PLINK
GWAS
updated 4 days ago by
GenoMax
151k • written 4 days ago by
sakura
▴ 40
3
votes
4
replies
355
views
bcftools not filtering snps
bcftools
3 days ago by
analyst
▴ 70
4
votes
2
replies
347
views
There are a way to align phage reads in to bacterial genomes?
alignment
sequences
reads
updated 5 days ago by
GenoMax
151k • written 5 days ago by
schlogl
▴ 180
4
votes
5
replies
553
views
No index in the undetermined fastq file
bcl2fastq
4 days ago by
1769mkc
★ 1.3k
121,269 results • Page
1 of 2426
Recent Votes
Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
Answer: Biological meaning of metrics commonly used for QC in scRNA-seq?
Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
Comment: Running Unicycler with a merged fastq file
Answer: pysam header and body
Comment: RagTag results
Answer: mitochondrial assamply use NOVOplasty
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Recent Replies
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…
Comment: Unsure whether or not I overcorrected for batch effect in dataset
by
cfos4698
★ 1.1k
It would help if you provided your code so others know what steps you took to batch-correct your data
Comment: Primer removal in amplicon sequencing
by
sxf520
• 0
Thanks. I actually want to know if I should use the full sequence (with the overhang part) or only the gene specific part as the primer se…
Comment: Primer removal in amplicon sequencing
by
GenoMax
151k
If you are looking to remove the primer sequences then you can provide these to scan/trim programs like `bbduk.sh` from BBMap suite or `fas…
Answer: GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no
by
Pierre Lindenbaum
166k
This question has been asked many times: https://www.biostars.org/p/9475152/ , https://www.biostars.org/p/146322/ , https://www.biostars.or…
Answer: Batch correction without biological covariates
by
swbarnes2
15k
Well, hopefully your batch variation has nothing to do with your biological variation. If they overlap, like all your controls are one b…
Comment: Random seed in scanpy
by
GenoMax
151k
Looks like random seed is used in: https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.umap.html and https://scanpy.readthedocs.io/…
Comment: finding gene sequence from WGS data
by
swbarnes2
15k
It's probably simpler to just make the whole altered consensus, then pick out what you want, instead of only making the consensus for 4 reg…
Comment: TCGA Germline allelic fraction distribution
by
ramiro.barrantes
▴ 50
By the way, this problem is solved. The issue was that TCGA is WXS data, and I was missing the appropriate parameter (--wes) on Strelka. On…
Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
by
jared.andrews07
★ 18k
Yeah, those clusters are suspicious. But if you feel the biology explains them appropriately, then lean on that knowledge. Just be prepared…
Comment: Still bad phred score after fastp
by
AIMAR
▴ 10
Hi I didn't really understand what's the problem, so if you can provide some images also the FastP command that you've used it could be hel…
Comment: Biological meaning of metrics commonly used for QC in scRNA-seq?
by
txema.heredia
▴ 240
Thanks! I'm basically doing the same as you. I have already annotated my clusters and I was re-checking the QC metrics and saw some cells …
Comment: Tools that output positions of matching kmers
by
GenoMax
151k
> As this is a standard step in almost every aligner But it is an intermediate step that most users are not interested in and it is used…
Comment: Still bad phred score after fastp
by
GenoMax
151k
If you can include screenshots of what you are referring to in text that would help get specific comments. In absence of the images, it sou…
Comment: RagTag results
by
shelkmike
★ 1.6k
If you read the manual of RagTag, you'll see that there is an option -r that makes RagTag to infer gap sizes from reference (https://github…
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