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121,273 results • Page
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Sort: Rank
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Views
Votes
Replies
0
votes
2
replies
77
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard
bwa
2 hours ago by
curious
▴ 890
0
votes
0
replies
56
views
use AverageExpression to stratify samples
scRNA
6 hours ago by
ndra1456
• 0
0
votes
0
replies
48
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
7 hours ago by
Wenhai
• 0
0
votes
0
replies
176
views
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clustering at 97%)
vsearch
updated 12 hours ago by
GenoMax
151k • written 13 hours ago by
salma.sarker
• 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
69
views
RepeatMasker output file question
RepeatMasker
16 hours ago by
xinguok794
• 0
1
vote
1
reply
334
views
Which GWAS tool to use that can work on Czech cases and British controls, on a binary trait?
plink2
gwas
saige
updated 19 hours ago by
LChart
4.9k • written 2 days ago by
anita.szabo08
▴ 10
0
votes
2
replies
148
views
Unsure whether or not I overcorrected for batch effect in dataset
Quality
Plot
PCA
Control
updated 4 hours ago by
GenoMax
151k • written 21 hours ago by
Megan
▴ 50
0
votes
3
replies
147
views
Primer removal in amplicon sequencing
removal
Primer
Amplicon
DADA2
sequencing
updated 9 hours ago by
GenoMax
151k • written 23 hours ago by
sxf520
• 0
0
votes
1
reply
162
views
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
GATK
VCF
BSQR
updated 1 day ago by
Ram
45k • written 1 day ago by
iamsmor
• 0
0
votes
1
reply
150
views
Batch correction without biological covariates
Combat-seq
RNA-seq
batch-correction
updated 1 day ago by
Ram
45k • written 1 day ago by
as823jk
• 0
0
votes
1
reply
129
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 1 day ago by
Ram
45k • written 1 day ago by
bioinfo
▴ 160
1
vote
3
replies
202
views
RagTag results
NGS
scaffolding
RagTag
gaps
updated 1 day ago by
shelkmike
★ 1.6k • written 1 day ago by
synthiiihuh
• 0
0
votes
1
reply
159
views
Tools that output positions of matching kmers
sequences
genomics
kmers
updated 1 day ago by
GenoMax
151k • written 1 day ago by
gil.hornung
▴ 100
2
votes
4
replies
266
views
mitochondrial assamply use NOVOplasty
mitochondrial
genome
mammles
updated 1 day ago by
cfos4698
★ 1.1k • written 2 days ago by
m90
▴ 30
0
votes
2
replies
181
views
Still bad phred score after fastp
phred
fastp
updated 1 day ago by
Ram
45k • written 1 day ago by
Shazel
• 0
0
votes
1
reply
155
views
Cytohubba problem and difference networks
Network
cytoscape
cytohubba
analysis
updated 1 day ago by
Scooter
▴ 310 • written 2 days ago by
mastorehpournazari
• 0
0
votes
1
reply
345
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
updated 1 day ago by
Scooter
▴ 310 • written 24 days ago by
Adrian
• 0
3
votes
1
reply
151
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 1 day ago by
GenoMax
151k • written 2 days ago by
biostars
▴ 30
2
votes
3
replies
243
views
Mass-spectrometry proteomics
Proteomics
analysis
11 hours ago by
Nasim Gandomdoust
• 0
7
votes
3
replies
270
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome
QC
velocity
single-cell
intron
updated 1 day ago by
jared.andrews07
★ 18k • written 2 days ago by
txema.heredia
▴ 240
0
votes
0
replies
107
views
News:
Eukaryotic eDNA Metabarcoding Course (14–18 July, Online)
Metabarcoding
eDNA
Genomics
Nanopore
2 days ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
276
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
591
views
miRNA low mapping(Qiagen miRNA Library Prep)
Qiagen
pipeline
trimming
alignment
miRNA
updated 1 day ago by
GenoMax
151k • written 5 days ago by
anthony.santana.703.j
• 0
0
votes
12
replies
882
views
STAR alignment not detecting some transcripts / custom reference
star
bwa
rna-seq
alignment
scrna-seq
updated 1 day ago by
rfran010
★ 1.5k • written 7 days ago by
npont
• 0
0
votes
0
replies
111
views
eHOMD database: Ref seq Aligned FASTA vs Full RefSeq?
HOMD
database
2 days ago by
bioinfo
▴ 60
2
votes
3
replies
354
views
pysam header and body
bam
pysam
view
updated 2 days ago by
dariober
15k • written 4 days ago by
Matteo Ungaro
▴ 120
3
votes
1
reply
264
views
Discrepency in assembly sizes
Pacbio
assembly
Kmer
updated 2 days ago by
shelkmike
★ 1.6k • written 4 days ago by
hpapoli
▴ 170
0
votes
1
reply
158
views
fasterq-dump fails before completing lookup
lookup
incomplete
fasterq-dump
updated 2 days ago by
GenoMax
151k • written 2 days ago by
nmannda148
• 0
4
votes
1
reply
196
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
2 days ago by
anna
▴ 40
0
votes
4
replies
309
views
ATACSEQ normlization for bigwig files
normalization
atac-seq
updated 3 days ago by
ATpoint
88k • written 3 days ago by
RD
▴ 20
4
votes
6
replies
407
views
finding gene sequence from WGS data
gene
WGS
updated 1 day ago by
swbarnes2
15k • written 3 days ago by
analyst
▴ 70
0
votes
0
replies
140
views
Question about Protein-protein-DNA complex prediction
prediction
protein
3 days ago by
mickley413
• 0
1
vote
10
replies
2.0k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 3 days ago by
s.faria
• 0 • written 2.7 years ago by
Gerard
▴ 10
2
votes
4
replies
600
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis
method
rnaseq
updated 3 days ago by
mbyvcm
▴ 460 • written 8 days ago by
cgibbsm
▴ 20
1
vote
2
replies
262
views
pddg+odgi+vg to perform pangenome analysis to cyanobacteria
odgi
pggb
help
pangenome
vg
updated 3 days ago by
GenoMax
151k • written 3 days ago by
snmdba
▴ 10
1
vote
2
replies
258
views
Comparing sets of genes for similarity
R
jaccard
genes
marker
clustering
1 day ago by
yura.grabovska
▴ 780
0
votes
0
replies
168
views
News:
Network Analysis in Systems Biology - 2 seats left
Bioconductor
SystemsBiology
R
NetworkAnalysis
RNAseq
3 days ago by
Physalia-courses
★ 2.6k
2
votes
5
replies
401
views
Running Unicycler with a merged fastq file
unicycler
bacterial-genome
assembly
updated 2 days ago by
GenoMax
151k • written 3 days ago by
Assa Yeroslaviz
★ 1.9k
2
votes
5
replies
439
views
Assemblers for short read bacterial isolates data
data
isolates
assembly
shotgun
updated 3 hours ago by
Mensur Dlakic
★ 29k • written 5 days ago by
shevch2009
▴ 20
0
votes
2
replies
296
views
Biopython get_terminals() doesn't get all terminals
biopython
tree
get_terminals
gtdb
4 days ago by
khp35
• 0
0
votes
0
replies
182
views
Covariate Selection for DESeq2/ANCOM-BC: Alpha vs. Beta Diversity Findings
ANCOM-BC
microbiome
covariates
DESeq2
PERMANOVA
4 days ago by
bioinfo
▴ 60
0
votes
1
reply
271
views
NF core rna-seq pipeline
nf-core
nextflow
pipeline
rnaseq
updated 4 days ago by
GenoMax
151k • written 4 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
192
views
Need Access to RadGraph2 Dataset from PhysioNet — Stuck at CITI Course Step
dataset
4 days ago by
z.mohammadi64
• 0
6
votes
3
replies
335
views
Both up- and down-regulated gene sets return the same GO pathway analysis results?
DEseq2
GO-analysis
2 days ago by
xqyn
▴ 60
0
votes
1
reply
241
views
Discrepancies calculatin average coverage with Bedtools and Mosdepth
mosdepth
human
bedtools
libraries
illumina
updated 4 days ago by
Pierre Lindenbaum
166k • written 4 days ago by
María José
▴ 10
4
votes
7
replies
3.6k
views
Michigan imputation server error
TOPMed
VCF
updated 4 days ago by
Joel Wallenius
▴ 220 • written 4.9 years ago by
AR
• 0
2
votes
8
replies
660
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant
Somatic_data
Help
Copy
1 day ago by
AIMAR
▴ 10
2
votes
2
replies
303
views
Error with bigWigAverageOverBed
usc
human
libraries
illumina
bigWigAverageOverBed
updated 4 days ago by
Pierre Lindenbaum
166k • written 4 days ago by
María José
▴ 10
8
votes
11
replies
628
views
de novo chromosome level assembly
genome
assembly
chromsome
updated 2 days ago by
lieven.sterck
15k • written 5 days ago by
mthm
▴ 80
121,273 results • Page
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Comment: Calculation of VAF (variant allele frequency)
A: Fold change - a final explanation
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Answer: Mass-spectrometry proteomics
Answer: Mass-spectrometry proteomics
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Recent Replies
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…
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…
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