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88 results • Page
2 of 2
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Votes
Replies
0
votes
1
reply
141
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
4 days ago by
asalimih
▴ 60
0
votes
0
replies
111
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
4 days ago by
jway
• 0
0
votes
1
reply
157
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 4 days ago by
Papyrus
★ 2.9k • written 4 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
153
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Lélé
▴ 10
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
0
votes
0
replies
99
views
ReactomeGSA
ReactomeGSA
5 days ago by
Shaimaa Gamal
▴ 10
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
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
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
2
replies
195
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
0
votes
0
replies
115
views
Is there a real ground truth for CNV data?
CNV
5 days ago by
jennyp0706
• 0
1
vote
1
reply
151
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
kilcdincer
▴ 10
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
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
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
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
0
votes
0
replies
107
views
reference-free assembly error assessment tools
assembly
6 days ago by
lagartija
▴ 160
0
votes
4
replies
269
views
Galaxy StringTie error
stringtie
galaxy
6 days ago by
trkfs
• 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
1
vote
4
replies
360
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 5 days ago by
Juke34
8.6k • written 7 days ago by
Vijith
▴ 30
0
votes
1
reply
166
views
consensus sequence calling
consensus
updated 6 days ago by
bk11
★ 2.5k • written 7 days ago by
Ghada
• 0
1
vote
2
replies
370
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 6 days ago by
Ram
43k • written 7 days ago by
t.fortunato.asquini
• 0
1
vote
4
replies
341
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 2 days ago by
Joe
21k • written 11 days ago by
cput
• 0
5
votes
7
replies
526
views
RNA seq analysis
DESeq
RNA-seq
5 days ago by
Jacek
▴ 20
1
vote
1
reply
192
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 3 days ago by
Jordan M Eizenga
▴ 460 • written 14 days ago by
sarumonsus
▴ 10
3
votes
3
replies
297
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 6 days ago by
Ram
43k • written 20 days ago by
Adyasha
• 0
0
votes
0
replies
127
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 6 days ago by
Ram
43k • written 21 days ago by
atharvakarkare14
▴ 40
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
6 days ago by
Emily
▴ 20
0
votes
2
replies
302
views
Traveler with Infernal mapping failed
r2dt
updated 1 day ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
9
replies
610
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
4 days ago by
Arton
▴ 10
2
votes
9
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
22 hours ago by
LauferVA
4.2k
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 6 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
88 results • Page
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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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