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54 results • Page
1 of 2
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Votes
Replies
4
votes
4
replies
2.8k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 1 hour ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
0
votes
2
replies
95
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 hour ago by
ATpoint
82k • written 11 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
50
views
How to access GWAVA software of data
GWAVA
updated 10 minutes ago by
GenoMax
142k • written 2 hours ago by
nonaddldy
▴ 10
0
votes
1
reply
91
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 5 hours ago by
ATpoint
82k • written 11 hours ago by
Chen
• 0
0
votes
1
reply
79
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 hours ago by
ATpoint
82k • written 9 hours ago by
Pegasus
▴ 100
0
votes
1
reply
71
views
What is the bin size for Bamcompare?
bin
chipseq
size
bamcompare
deeptools
updated 5 hours ago by
ATpoint
82k • written 8 hours ago by
Emily
▴ 20
1
vote
1
reply
102
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 5 hours ago by
zx8754
11k • written 12 hours ago by
ohtang7
▴ 40
0
votes
0
replies
38
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
6 hours ago by
Spring
• 0
0
votes
2
replies
88
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 hours ago by
IdaHao0921
• 0
0
votes
3
replies
266
views
Snakemake wrapper issue
fastqc
snakemake
6 hours ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
57
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
9 hours ago by
Holly
• 0
2
votes
5
replies
185
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 9 hours ago by
Philipp Bayer
8.5k • written 12 hours ago by
林明德
• 0
0
votes
4
replies
2.2k
views
MGLTools does not work in windows 11
Autodock
MGLTools
windows
windows11
updated 9 hours ago by
Ashfaq
• 0 • written 13 months ago by
mohyeddine.taleb
• 0
0
votes
1
reply
88
views
Filtering based on alternate allelic balance
GATK
Bioinformatics
Filter
VCF
12 hours ago by
Arton
• 0
0
votes
0
replies
54
views
Biomart issue, why so few 3'utrs?
utr
biomart
12 hours ago by
RNAseqer
▴ 270
1
vote
4
replies
128
views
Help with IGV abbreviation
Genome
browser
11 hours ago by
GeneC
• 0
0
votes
1
reply
109
views
How to process Bulk WES data?
WES
WGS
updated 14 hours ago by
GenoMax
142k • written 15 hours ago by
wyuan37
• 0
0
votes
1
reply
108
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 13 hours ago by
GenoMax
142k • written 16 hours ago by
cedric.blais
• 0
0
votes
2
replies
379
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
16 hours ago by
David Langenberger
11k
0
votes
1
reply
94
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 15 hours ago by
Ram
43k • written 17 hours ago by
eking28
• 0
1
vote
4
replies
361
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 16 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
321
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
17 hours ago by
kalavattam
▴ 190
1
vote
2
replies
178
views
How to interpret infinite odds ratio?
statistics
2 hours ago by
Lukas
• 0
1
vote
2
replies
123
views
Duplicated sequence samtools
bowtie2
samtools
updated 18 hours ago by
GenoMax
142k • written 19 hours ago by
Moinuddin
• 0
0
votes
0
replies
66
views
reference-free assembly error assessment tools
assembly
19 hours ago by
lagartija
▴ 160
1
vote
2
replies
159
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 19 hours ago by
lagartija
▴ 160 • written 1 day ago by
Esraa
• 0
1
vote
0
replies
68
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
20 hours ago by
J.
▴ 10
0
votes
0
replies
86
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
20 hours ago by
Biostar
2.7k
0
votes
1
reply
97
views
Splitting Seurat object by sample layers
seurat
updated 15 hours ago by
Ram
43k • written 21 hours ago by
kilcdincer
▴ 10
0
votes
4
replies
169
views
Galaxy StringTie error
stringtie
galaxy
2 hours ago by
trkfs
• 0
0
votes
0
replies
70
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
23 hours ago by
atariw
▴ 10
0
votes
1
reply
118
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 23 hours ago by
GenoMax
142k • written 1 day ago by
octpus616
▴ 100
1
vote
3
replies
182
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
4 hours ago by
Vijith
▴ 30
0
votes
1
reply
119
views
consensus sequence calling
consensus
updated 20 hours ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
3
replies
143
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 15 hours ago by
Ram
43k • written 1 day ago by
yau
• 0
3
votes
2
replies
233
views
imputation through beagle
panel
beagle
reference
imputation
4 hours ago by
analyst
▴ 50
2
votes
4
replies
252
views
BWA alignment
Samtools
bam
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Vahid
• 0
0
votes
1
reply
224
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 14 hours ago by
Ram
43k • written 4 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 hour ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
1
vote
2
replies
329
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 21 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
3
votes
3
replies
308
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 13 hours ago by
Mathew
▴ 130 • written 3 days ago by
Christopher
• 0
0
votes
6
replies
377
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 15 hours ago by
Ram
43k • written 3 days ago by
ajbarrett98
• 0
0
votes
5
replies
295
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
23 hours ago by
SilhouetteQ
• 0
1
vote
4
replies
324
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 15 hours ago by
Ram
43k • written 5 days ago by
samRayne
• 0
4
votes
6
replies
400
views
RNA seq analysis
DESeq
RNA-seq
updated 23 hours ago by
Matthias Zepper
4.6k • written 6 days ago by
prifa
▴ 10
0
votes
1
reply
137
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Cancer-Research
ATAC-seq
updated 14 hours ago by
Ram
43k • written 7 days ago by
David
• 0
0
votes
3
replies
335
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
17 hours ago by
mropri
▴ 150
4
votes
7
replies
378
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
12 hours ago by
Chen
• 0
3
votes
3
replies
252
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 14 hours ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
0
votes
0
replies
111
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 14 hours ago by
Ram
43k • written 15 days ago by
atharvakarkare14
▴ 30
54 results • Page
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Recent Votes
Comment: Help with IGV abbreviation
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
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Recent Replies
Comment: How to access GWAVA software of data
by
GenoMax
142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection
by
Anitha
• 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object
by
ATpoint
82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error
by
trkfs
• 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio?
by
Lukas
• 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Comment: How to access GWAVA software of data
by
nonaddldy
▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
by
IdaHao0921
• 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Vijith
▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment
by
ATpoint
82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation
by
ATpoint
82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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