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13,055 results • Page
1 of 262
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Votes
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0
votes
3
replies
9
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
just now by
Esraa
• 0
0
votes
0
replies
8
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
13 minutes ago by
egascon
• 0
0
votes
1
reply
43
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
Alexandra
• 0
1
vote
1
reply
126
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 2 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
0
votes
1
reply
72
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
updated 2 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
Arton
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
28
views
ReactomeGSA
ReactomeGSA
2 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
28
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
2 hours ago by
Transmitting Science communication
▴ 70
0
votes
0
replies
42
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
4 hours ago by
njornet
▴ 20
0
votes
0
replies
33
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmap
bbmerge
4 hours ago by
chrisk
• 0
0
votes
0
replies
49
views
Forum:
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
6 hours ago by
iqra
• 0
0
votes
0
replies
53
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 8 hours ago by
GenoMax
142k • written 9 hours ago by
Dude
• 0
0
votes
0
replies
47
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
9 hours ago by
brunofelicianodeomena
• 0
1
vote
2
replies
124
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 hours ago by
colindaven
6.4k • written 10 hours ago by
mbrav005
• 0
0
votes
1
reply
93
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
6 hours ago by
sansan_96
▴ 90
0
votes
1
reply
98
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 12 hours ago by
Mensur Dlakic
★ 27k • written 13 hours ago by
MarcosCosta
• 0
2
votes
2
replies
159
views
Genome Visualization Tools
bacterial
genome
updated 14 hours ago by
GenoMax
142k • written 14 hours ago by
dlera.lozano
▴ 10
1
vote
3
replies
161
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 13 hours ago by
Ram
43k • written 14 hours ago by
Prawesh
• 0
0
votes
2
replies
177
views
Using ggplotly in R
ggplot
ggplotly
7 hours ago by
jen
▴ 10
0
votes
1
reply
129
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
bioinfo
▴ 150
0
votes
3
replies
209
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 16 hours ago by
noodle
▴ 580 • written 20 hours ago by
doramora
▴ 10
0
votes
1
reply
113
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 17 hours ago by
LauferVA
4.2k • written 18 hours ago by
graeme.thorn
▴ 100
0
votes
2
replies
128
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 hours ago by
melissa.joubert
• 0
0
votes
0
replies
81
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
18 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
170
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
20 hours ago by
J.
▴ 40
0
votes
0
replies
83
views
Is there a real ground truth for CNV data?
CNV
21 hours ago by
jennyp0706
• 0
0
votes
3
replies
175
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
115
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 16 hours ago by
Ram
43k • written 21 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
74
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 21 hours ago by
GenoMax
142k • written 22 hours ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 23 hours ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
340
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
7 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
177
views
How to access GWAVA software of data
GWAVA
updated 22 hours ago by
GenoMax
142k • written 1 day ago by
nonaddldy
▴ 10
0
votes
1
reply
148
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Chen
• 0
1
vote
1
reply
152
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
117
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 13 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
1
vote
1
reply
164
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
81
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
2
replies
158
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
3
replies
319
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
238
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day 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 13 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
190
views
Help with IGV abbreviation
igv
updated 13 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
0
votes
1
reply
150
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
146
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
2
replies
414
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
1 day ago by
David Langenberger
11k
0
votes
1
reply
136
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 1 day ago by
Ram
43k • written 1 day ago by
eking28
• 0
1
vote
5
replies
464
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 13 hours ago by
Ram
43k • written 6 days ago by
Prawesh
• 0
1
vote
3
replies
416
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
1
vote
2
replies
251
views
How to interpret infinite odds ratio?
statistics
1 day ago by
Lukas
• 0
1
vote
2
replies
162
views
Duplicated sequence samtools
bowtie2
samtools
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Moinuddin
• 0
13,055 results • Page
1 of 262
Recent Votes
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
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Recent Replies
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…
Answer: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
melissa.joubert
• 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
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