Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
44 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
0
views
Add stats to boxplot in R
stats
R
just now by
Ghada
• 0
0
votes
1
reply
29
views
calculating genomic coverage/ base overlap in R
bioinoformatics
genomics
updated 40 minutes ago by
marco.barr
▴ 110 • written 55 minutes ago by
Sayantani
• 0
0
votes
2
replies
34
views
Annotating file using bcftools
annotation
plink
bcftools
updated 43 minutes ago by
Pierre Lindenbaum
161k • written 2 hours ago by
kl
▴ 10
0
votes
0
replies
24
views
genome finishing
finishing
genome
1 hour ago by
trezini
• 0
0
votes
3
replies
94
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
updated 52 minutes ago by
marco.barr
▴ 110 • written 6 hours ago by
njornet
▴ 20
0
votes
3
replies
68
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 hours ago by
Esraa
• 0
0
votes
1
reply
62
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
egascon
• 0
1
vote
1
reply
75
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 3 hours ago by
ATpoint
82k • written 4 hours ago by
Alexandra
• 0
1
vote
1
reply
160
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 4 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
0
votes
1
reply
89
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
updated 4 hours ago by
Pierre Lindenbaum
161k • written 8 hours ago by
Arton
• 0
0
votes
0
replies
41
views
ReactomeGSA
ReactomeGSA
4 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
40
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
5 hours ago by
Transmitting Science communication
▴ 70
0
votes
1
reply
58
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 hour ago by
GenoMax
142k • written 6 hours ago by
chrisk
• 0
0
votes
0
replies
54
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 hour ago by
GenoMax
142k • written 9 hours ago by
iqra
• 0
0
votes
0
replies
56
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
Dude
• 0
0
votes
0
replies
52
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
11 hours ago by
brunofelicianodeomena
• 0
1
vote
2
replies
139
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 6 hours ago by
colindaven
6.4k • written 13 hours ago by
mbrav005
• 0
0
votes
1
reply
101
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
9 hours ago by
sansan_96
▴ 90
0
votes
1
reply
101
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 15 hours ago by
MarcosCosta
• 0
2
votes
2
replies
163
views
Genome Visualization Tools
bacterial
genome
updated 16 hours ago by
GenoMax
142k • written 17 hours ago by
dlera.lozano
▴ 10
1
vote
3
replies
164
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 15 hours ago by
Ram
43k • written 17 hours ago by
Prawesh
• 0
0
votes
2
replies
182
views
Using ggplotly in R
ggplot
ggplotly
9 hours ago by
jen
▴ 10
0
votes
1
reply
132
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 17 hours ago by
GenoMax
142k • written 18 hours ago by
bioinfo
▴ 150
0
votes
3
replies
213
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 18 hours ago by
noodle
▴ 580 • written 22 hours ago by
doramora
▴ 10
0
votes
1
reply
116
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 19 hours ago by
LauferVA
4.2k • written 20 hours ago by
graeme.thorn
▴ 100
0
votes
2
replies
142
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
5 hours ago by
melissa.joubert
• 0
0
votes
0
replies
83
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
20 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
173
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
22 hours ago by
J.
▴ 40
0
votes
0
replies
85
views
Is there a real ground truth for CNV data?
CNV
23 hours ago by
jennyp0706
• 0
0
votes
3
replies
180
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
119
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 18 hours ago by
Ram
43k • written 23 hours ago by
kilcdincer
▴ 10
1
vote
7
replies
347
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
9 hours ago by
ntsopoul
▴ 60
0
votes
1
reply
120
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 15 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 16 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
193
views
Help with IGV abbreviation
igv
updated 15 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
1
vote
5
replies
468
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 15 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
2
votes
4
replies
268
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
5 hours ago by
Esraa
• 0
1
vote
4
replies
325
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 11 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
2
votes
6
replies
352
views
BWA alignment
Samtools
bam
updated 7 hours ago by
a.alnawfal.1992
▴ 260 • written 2 days ago by
Vahid
• 0
2
votes
9
replies
660
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 4 hours ago by
Pierre Lindenbaum
161k • written 7 days ago by
schmince
• 0
4
votes
7
replies
453
views
RNA seq analysis
DESeq
RNA-seq
4 hours ago by
Jacek
▴ 10
0
votes
8
replies
537
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
5 hours ago by
JACKY
▴ 140
2
votes
3
replies
268
views
Finding variants within a subset of a BAM file
variant
calling
21 hours ago by
ramiro.barrantes
• 0
5
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing
coverage
8 hours ago by
Arton
• 0
44 results • Page
1 of 1
Recent Votes
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Recent Locations •
All
France,
1 minute ago
Japan,
1 minute ago
United States,
1 minute ago
moon,
3 minutes ago
Netherlands,
3 minutes ago
Russia,
3 minutes ago
Germany,
5 minutes ago
Recent Awards •
All
Popular Question
to
rj.rezwan
• 0
Popular Question
to
matteo.levorato
• 0
Popular Question
to
Palgrave
▴ 110
Popular Question
to
DBScan
▴ 300
Popular Question
to
chrisk
• 0
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Recent Replies
Answer: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Annotating file using bcftools
by
Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
I had the same problem in this iusse [https://github.com/nanoporetech/dorado/issues/603][1] and I solved it as they say here [1]: https…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
ATpoint
82k
Looking at this briefly, it is small sample size and you do not correct for any potential confounders. Use PCA or MDS to explore the data. …
Comment: bbmerge (bbmap) ~ error with insert size file output
by
GenoMax
142k
> It is confirmed (and solved in another thread) that we have significant overlapping paired end reads. Can you provide a reference to sai…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
> I get the exact same read with the same ID and all more than once If you have short(er) reads you could be seeing secondary alignments. …
Answer: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data
by
i.sudbery
19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
**My references** Genome: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_al…
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
ATpoint
82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis
by
Jacek
▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
by
dariober
14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Traffic: 2645 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6