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184 results • Page
3 of 4
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Views
Votes
Replies
0
votes
3
replies
172
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
5 days ago by
Esraa
• 0
3
votes
3
replies
237
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Alexandra
• 0
3
votes
1
reply
332
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 5 days ago by
dariober
14k • written 6 days ago by
Holly
▴ 30
1
vote
4
replies
298
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
4 days ago by
Arton
▴ 10
0
votes
0
replies
99
views
ReactomeGSA
ReactomeGSA
5 days ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
88
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
5 days ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
291
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 4 days ago by
GenoMax
142k • written 5 days ago by
chrisk
• 0
0
votes
1
reply
177
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 4 days ago by
DGTool
▴ 20 • written 5 days ago by
iqra
• 0
0
votes
0
replies
100
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Dude
• 0
0
votes
0
replies
98
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
5 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
213
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 5 days ago by
colindaven
6.4k • written 5 days ago by
mbrav005
• 0
0
votes
1
reply
151
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
5 days ago by
sansan_96
▴ 90
1
vote
2
replies
235
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
4 days ago by
MarcosCosta
• 0
2
votes
2
replies
209
views
Genome Visualization Tools
bacterial
genome
updated 5 days ago by
GenoMax
142k • written 5 days ago by
dlera.lozano
▴ 10
2
votes
3
replies
219
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
298
views
Using ggplotly in R
ggplot
ggplotly
updated 4 days ago by
jared.andrews07
★ 16k • written 5 days ago by
jen
▴ 10
1
vote
2
replies
235
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
3 days ago by
bioinfo
▴ 150
0
votes
3
replies
271
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 5 days ago by
noodle
▴ 580 • written 5 days ago by
doramora
▴ 10
0
votes
1
reply
149
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 5 days ago by
LauferVA
4.2k • written 5 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
196
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
5 days ago by
melissa.joubert
• 0
4
votes
1
reply
213
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
5 days ago by
J.
▴ 40
0
votes
0
replies
115
views
Is there a real ground truth for CNV data?
CNV
5 days ago by
jennyp0706
• 0
0
votes
3
replies
222
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 6 days ago by
GenoMax
142k • written 6 days ago by
RNAseqer
▴ 270
1
vote
1
reply
151
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 5 days ago by
Ram
43k • written 6 days ago by
kilcdincer
▴ 10
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 6 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
8
replies
472
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 2 days ago by
Alex Reynolds
35k • written 6 days ago by
ntsopoul
▴ 60
0
votes
3
replies
215
views
How to access GWAVA software of data
GWAVA
updated 6 days ago by
GenoMax
142k • written 6 days ago by
nonaddldy
▴ 10
0
votes
2
replies
232
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
4 days ago by
Chen
• 0
1
vote
1
reply
178
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Pegasus
▴ 100
0
votes
1
reply
136
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 5 days ago by
Ram
43k • written 6 days ago by
Emily
▴ 20
1
vote
3
replies
284
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 3 days ago by
GenoMax
142k • written 6 days ago by
ohtang7
▴ 40
0
votes
0
replies
96
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
6 days ago by
Spring
• 0
0
votes
2
replies
190
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
6 days ago by
IdaHao0921
• 0
0
votes
3
replies
359
views
Snakemake wrapper issue
fastqc
snakemake
updated 6 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
290
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 6 days ago by
Philipp Bayer
8.5k • written 6 days ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 5 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
239
views
Help with IGV abbreviation
igv
updated 5 days ago by
Ram
43k • written 6 days ago by
GeneC
• 0
0
votes
1
reply
166
views
How to process Bulk WES data?
WES
WGS
updated 6 days ago by
GenoMax
142k • written 6 days ago by
wyuan37
• 0
0
votes
1
reply
164
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 6 days ago by
GenoMax
142k • written 6 days ago by
cedric.blais
• 0
0
votes
2
replies
442
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
6 days ago by
David Langenberger
11k
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 6 days ago by
Ram
43k • written 6 days ago by
eking28
• 0
2
votes
5
replies
520
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 5 days ago by
Ram
43k • written 11 days ago by
Prawesh
• 0
1
vote
3
replies
453
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
6 days ago by
kalavattam
▴ 190
1
vote
2
replies
271
views
How to interpret infinite odds ratio?
statistics
6 days ago by
Lukas
• 0
4
votes
2
replies
197
views
Duplicated sequence samtools
bowtie2
samtools
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Moinuddin
• 0
0
votes
0
replies
107
views
reference-free assembly error assessment tools
assembly
6 days ago by
lagartija
▴ 160
2
votes
4
replies
311
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
5 days ago by
Esraa
• 0
2
votes
0
replies
146
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
6 days ago by
Biostar
2.8k
0
votes
1
reply
146
views
Splitting Seurat object by sample layers
seurat
updated 6 days ago by
Ram
43k • written 6 days ago by
kilcdincer
▴ 10
0
votes
4
replies
269
views
Galaxy StringTie error
stringtie
galaxy
6 days ago by
trkfs
• 0
184 results • Page
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Answer: Ti Tv ratio and their usefulness in exome sequencing
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Answer: How do you generate TMM normalized counts using EdgeR?
Analysing Microarray Data In Bioconductor
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Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot
by
marco.barr
▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot
by
Ghada
• 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R
by
marco.barr
▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
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