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395 results • Page
5 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
126
views
Merging replicates from Encode project
CHIP-seq
encode
21 days ago by
Nurken
• 0
1
vote
3
replies
291
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
21 days ago by
WouterDeCoster
47k
1
vote
3
replies
328
views
some error in building kraken2 database
metagenome
kraken2
20 days ago by
Art1ess
• 0
0
votes
1
reply
205
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 20 days ago by
bk11
★ 2.4k • written 21 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
209
views
Failed kmer content
kmer
illumina
ngs
updated 20 days ago by
Ram
43k • written 21 days ago by
Kasturi
• 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 20 days ago by
Ram
43k • written 21 days ago by
SSSJec
• 0
0
votes
1
reply
173
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 21 days ago by
Ram
43k • written 21 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
445
views
Error in cnetplot enrichplot package
R
updated 21 days ago by
Ram
43k • written 21 days ago by
Farhad
• 0
0
votes
0
replies
128
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 21 days ago by
Ram
43k • written 21 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 21 days ago by
Ram
43k • written 21 days ago by
sansan_96
▴ 90
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 20 days ago by
Ram
43k • written 21 days ago by
Amélie
• 0
0
votes
0
replies
222
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 21 days ago by
Ram
43k • written 21 days ago by
Pine
▴ 20
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 21 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
523
views
Downsampling fastq file
downsample
fastq
13 days ago by
marco.barr
▴ 110
0
votes
1
reply
167
views
tbtool
tbtool
updated 21 days ago by
Ram
43k • written 21 days ago by
Raman
• 0
0
votes
10
replies
600
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 14 days ago by
i.sudbery
19k • written 21 days ago by
Patadu94
• 0
0
votes
1
reply
157
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 21 days ago by
ATpoint
82k • written 21 days ago by
enanoide
• 0
0
votes
0
replies
103
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
21 days ago by
manaswwm
▴ 510
0
votes
0
replies
96
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
21 days ago by
alifafiq1
• 0
0
votes
0
replies
100
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
22 days ago by
feather-W
• 0
2
votes
4
replies
367
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
20 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
98
views
Annotating single cell data automatically
cell
annotation
single
22 days ago by
Gerard
• 0
0
votes
1
reply
195
views
RNA-seq bacteria contamination
RNA-seq
updated 21 days ago by
GenoMax
142k • written 22 days ago by
sh
• 0
0
votes
0
replies
95
views
Imputation advice
imputation
22 days ago by
kl
▴ 10
0
votes
0
replies
115
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
22 days ago by
Enrique
• 0
0
votes
0
replies
91
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
22 days ago by
sativus
▴ 20
0
votes
0
replies
96
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
22 days ago by
Biostars2200
• 0
0
votes
0
replies
155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 22 days ago by
Carlo Yague
8.7k • written 22 days ago by
Atul K.
• 0
2
votes
5
replies
528
views
Marking duplicates using UMIs
Deduplication
UMI
updated 22 days ago by
i.sudbery
19k • written 23 days ago by
Lipika
• 0
0
votes
0
replies
156
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 22 days ago by
Ram
43k • written 23 days ago by
sainavyav22
• 0
0
votes
0
replies
160
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
23 days ago by
rthapa
▴ 90
0
votes
0
replies
155
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
23 days ago by
Mamatha Y S
• 0
0
votes
2
replies
315
views
bam merging for archaic samples
samtools
bam
updated 22 days ago by
Ram
43k • written 23 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
560
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
24 days ago by
mathavanbioinfo
▴ 90
2
votes
5
replies
776
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 23 days ago by
Jesse
▴ 770 • written 24 days ago by
Ann
★ 2.4k
0
votes
0
replies
204
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 24 days ago by
Ram
43k • written 24 days ago by
mja
• 0
0
votes
0
replies
206
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
24 days ago by
Nitin
• 0
0
votes
0
replies
198
views
Chemical structure validation
structure
cap
validation
metabolite
24 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
296
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 24 days ago by
GenoMax
142k • written 24 days ago by
bioyas
▴ 10
0
votes
0
replies
230
views
Copy number variation plot
Copy-number-variation
genomics
updated 24 days ago by
Ram
43k • written 24 days ago by
Emmi
• 0
0
votes
0
replies
207
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
24 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
319
views
Could you please assist in identifying this cluster?
single-cell
updated 24 days ago by
Ram
43k • written 24 days ago by
carolofharvest
▴ 40
0
votes
0
replies
223
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 24 days ago by
Ram
43k • written 25 days ago by
Dinmukhamed
• 0
0
votes
0
replies
215
views
miRDeep2: How to get the read counts
mirdeep2
25 days ago by
Atul K.
• 0
0
votes
0
replies
219
views
Lncipedia GTF file error
Proteomics
updated 24 days ago by
Ram
43k • written 25 days ago by
atharvakarkare14
▴ 30
3
votes
3
replies
545
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 24 days ago by
swbarnes2
14k • written 25 days ago by
noodle
▴ 580
0
votes
2
replies
588
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
25 days ago by
航太郎
• 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 25 days ago by
GenoMax
142k • written 25 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
419
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
25 days ago by
Ashok
• 0
0
votes
2
replies
462
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
25 days ago by
Ashok
• 0
395 results • Page
5 of 8
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: 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…
Answer: CNVkit for somatic copy number detection
by
Anitha
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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
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Anitha
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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
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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
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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 …
Answer: How to access GWAVA software of data
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nonaddldy
▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
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https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK
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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,…
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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…
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By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
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I have tried installing AGAT. But it failed the tests. …
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That is not what the logs above tell, but good you solved it.
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The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
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