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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
137
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
4 days ago by
Javier
• 0
0
votes
1
reply
231
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Thanujay S
• 0 • written 4 days ago by
yahn
• 0
0
votes
0
replies
130
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
4 days ago by
mikemakaveli1
• 0
2
votes
2
replies
215
views
Raw counts using stringtie
stringtie
RNA-seq
updated 4 days ago by
GenoMax
142k • written 5 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
130
views
Modify plot R mtDNA indel
plot
mtDNA
R
5 days ago by
marco.barr
▴ 90
0
votes
0
replies
321
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
5 days ago by
NorbertK
• 0
0
votes
2
replies
247
views
Downloading older version of a tool
Alignment
tools
4 days ago by
Ruqaiya
• 0
0
votes
0
replies
147
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
5 days ago by
rustykb
▴ 20
3
votes
5
replies
282
views
Generating mpileup file using samtools
mpileup
samtools
updated 5 days ago by
Joe
21k • written 5 days ago by
Ruqaiya
• 0
2
votes
3
replies
286
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 5 days ago by
dthorbur
★ 1.9k • written 5 days ago by
Vijith
▴ 30
0
votes
0
replies
145
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
5 days ago by
Jeyong
• 0
0
votes
0
replies
134
views
Empty table plot using plotGseaTable()
FGSEA
4 days ago by
Chris
▴ 280
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 5 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
198
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
5 days ago by
dtnondorf
• 0
1
vote
7
replies
513
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 17 hours ago by
Chris Dean
▴ 400 • written 5 days ago by
sovrappensiero
▴ 90
3
votes
8
replies
508
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
1 day ago by
Qroid
▴ 40
0
votes
1
reply
151
views
Provean help
variant
Provean
updated 5 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
101
views
Use of annotation of integrated Seurat object in single sample
Seurat
6 days ago by
Bine
▴ 60
0
votes
1
reply
229
views
Subsetting and merging back Seurat Object brings different results
Seurat
6 days ago by
Bine
▴ 60
1
vote
1
reply
143
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 5 days ago by
Ram
43k • written 6 days ago by
marco.barr
▴ 90
0
votes
0
replies
97
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
6 days ago by
Vijith
▴ 30
0
votes
0
replies
99
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
6 days ago by
James
▴ 10
0
votes
1
reply
588
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 6 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
241
views
Odd alignment question/finding
Alignment
updated 5 days ago by
barslmn
★ 2.1k • written 6 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
209
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 6 days ago by
GenoMax
142k • written 6 days ago by
mgranada3
▴ 30
0
votes
0
replies
101
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
6 days ago by
meck
• 0
0
votes
0
replies
126
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 6 days ago by
Ram
43k • written 6 days ago by
Oscar
▴ 10
0
votes
1
reply
153
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 6 days ago by
Ram
43k • written 6 days ago by
ernestine.kubi
• 0
0
votes
0
replies
107
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
6 days ago by
VITALA
• 0
1
vote
2
replies
257
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
6 days ago by
rianna.collins
• 0
0
votes
1
reply
191
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 7 days ago by
i.sudbery
19k • written 7 days ago by
Edmond
• 0
0
votes
0
replies
148
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
7 days ago by
O.rka
▴ 720
0
votes
1
reply
685
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 7 days ago by
Ram
43k • written 7 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
382
views
Telescope issue
Telescope
RNA-seq
updated 6 days ago by
GenoMax
142k • written 7 days ago by
eleven11
• 0
1
vote
1
reply
238
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 7 days ago by
Ram
43k • written 7 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
297
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
7 days ago by
Nafi
• 0
1
vote
3
replies
288
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 7 days ago by
GenoMax
142k • written 7 days ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
228
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
1 day ago by
Ahiad Chen Zion
• 0
0
votes
0
replies
128
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 8 days ago by
Ram
43k • written 8 days ago by
Alexandros
• 0
0
votes
1
reply
176
views
unable to get feature count results
featureCounts
updated 7 days ago by
Ram
43k • written 8 days ago by
Ravita
• 0
0
votes
3
replies
292
views
KEGG Pathways
r
RNA-seq
updated 7 days ago by
Ram
43k • written 8 days ago by
Sudip
• 0
0
votes
0
replies
136
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
8 days ago by
Bine
▴ 60
1
vote
2
replies
229
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 7 days ago by
Ram
43k • written 8 days ago by
Ravita
• 0
3
votes
3
replies
224
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
8 days ago by
fanglujing
▴ 60
0
votes
0
replies
136
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
8 days ago by
Jacob
• 0
0
votes
1
reply
185
views
Differential Accessibility
DiffBind
updated 8 days ago by
Ram
43k • written 8 days ago by
Shloka
• 0
0
votes
3
replies
298
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 8 days ago by
GenoMax
142k • written 8 days ago by
kim
• 0
3
votes
7
replies
355
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
8 days ago by
salias
• 0
0
votes
0
replies
129
views
Using limma in methylation EM-seq?
EM-seq
methylation
8 days ago by
Lluís R.
★ 1.2k
1,000 results • Page
2 of 20
Recent Votes
A: How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
How Do Heterozygotes And Somatic Mutations Manifest In Sequencing Projects
A: How to download genome assemblies from NCBI with a list of GCA identifiers?
How to download genome assemblies from NCBI with a list of GCA identifiers?
Answer: Why is RNA-Seq library size not constant among samples?
Answer: TFs and Gene databases
Answer: java out of memory error through beagle for imutation
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Recent Replies
Answer: How can I analyze normalized expression data?
by
Bastien Hervé
5.3k
This has been issued a dozen times before. Have a look at Limma package. https://support.bioconductor.org/p/126817/ https://support.bioco…
Comment: Error in plotting PCA plot in seurat
by
Bastien Hervé
5.3k
Without your code, it is impossible to make any statement. Please provide the code generating that issue. By googling, here is a [similar …
Comment: A question about reference genome for creating the consensus sequence
by
me
• 0
Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I in…
Comment: PseudobulkExpression.Seurat error
by
Bastien Hervé
5.3k
> None of the requested assays are present in the object Does the assay `originalexp` exist in your object `seurat_from_cds` ?
Comment: identifying transgene insertion site in WGS
by
Cameron.walker9900
• 0
When calling for SVs using gridds, should I use the reference genome that I added my transgene to, or should I use the unedited reference?
Comment: Question regarding WGCNA
by
deepak
• 0
Thank for the reply. I am running this code: # set a set of soft-thresholding powers powers = c(c(1:20), seq(from = 22, to=30, by=2)) # Ca…
Comment: RNA seq analysis
by
prifa
• 0
thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
Comment: RNA seq analysis
by
Matthias Zepper
4.6k
That you have a varying number of replicates is not ideal ([see here why][1]), but manageable. See for example the [Specific experimental d…
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
OK, in that case it should be even easier as its just a single pairwise alignment, so the same advice holds.
Comment: FarmCPU - how to explain the reported 'effect'?
by
chloek88
• 0
Hi Phillip, Did you ever figure out the answer to this? I also have rMVP results with a column 'effect', values ranging from ~-1.4 to +1…
Comment: Soft-clipping read ends based on read group
by
chenl
▴ 10
Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
Comment: A question about reference genome for creating the consensus sequence
by
GenoMax
142k
> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into http…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
GenoMax
142k
We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) da…
Answer: TFs and Gene databases
by
b.contreras.moreira
▴ 180
I can also suggest <https://footprintdb.eead.csic.es> which links TFs to their DNA motifs, not their gene targets.
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