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82 results • Page
1 of 2
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0
votes
0
replies
3
views
genomic region of transcription factor
search
HOMER
motif
3 minutes ago by
qudrat.nii
▴ 10
1
vote
4
replies
176
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
1 hour ago by
BATMAN
• 0
0
votes
4
replies
60
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
56 minutes ago by
hannes.bongartz
• 0
0
votes
0
replies
38
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 3 hours ago by
GenoMax
142k • written 4 hours ago by
yura.grabovska
▴ 90
0
votes
0
replies
47
views
constructing pangenome through psvcp
psvcp
pangenome
6 hours ago by
analyst
▴ 50
1
vote
9
replies
201
views
zero TPM for many gene including housekeeping when using kallisto
RNAseq
13 minutes ago by
ashkan
▴ 160
0
votes
1
reply
78
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 5 hours ago by
dthorbur
★ 2.0k • written 7 hours ago by
Umer
▴ 50
0
votes
2
replies
146
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 8 hours ago by
Pierre Lindenbaum
161k • written 15 hours ago by
melissachua90
▴ 70
0
votes
0
replies
54
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
10 hours ago by
Varsha
• 0
0
votes
1
reply
159
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 6 hours ago by
GenoMax
142k • written 13 hours ago by
huxiangyulove
• 0
0
votes
0
replies
71
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
17 hours ago by
O.rka
▴ 720
0
votes
4
replies
247
views
Merge clusters in Seurat UMAP
seurat
umap
8 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
76
views
Use of ichor CNA
Dog
CNA
genome
22 hours ago by
sainavyav22
• 0
2
votes
2
replies
187
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 20 hours ago by
Ram
43k • written 23 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
82
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
1
reply
132
views
How can I calculate the OS of each patient?
overall-survival
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pedro
• 0
0
votes
0
replies
81
views
cat-bgen fail
bgenix
updated 1 day ago by
Ram
43k • written 1 day ago by
lambard
• 0
1
vote
1
reply
139
views
API kegg - IndexError: list index out of range
kegg
API
updated 13 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
mirwa.zidi93
• 0
0
votes
0
replies
89
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
1 day ago by
ebertomeup
• 0
0
votes
3
replies
222
views
Sam file Header problem
Sam
Header
problem
file
updated 9 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
saifulislam99121
• 0
0
votes
0
replies
103
views
select set of intervals that cover a genomic region
GRanges
bed
1 day ago by
ntsopoul
▴ 60
0
votes
1
reply
130
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 11 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Luqman
• 0
0
votes
3
replies
171
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
updated 20 minutes ago by
andres.firrincieli
3.6k • written 1 day ago by
mavy
▴ 10
0
votes
1
reply
157
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 1 day ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
1
reply
147
views
Add line under stat test
stats
R
updated 12 hours ago by
Nyksubuz
▴ 20 • written 1 day ago by
Ghada
• 0
0
votes
0
replies
107
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
14
replies
613
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
10 hours ago by
hophuquy0944
• 0
0
votes
1
reply
139
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
2 days ago by
asalimih
▴ 60
0
votes
0
replies
109
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
2 days ago by
jway
• 0
0
votes
1
reply
146
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 1 day ago by
Papyrus
★ 2.9k • written 2 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
148
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 1 day ago by
GenoMax
142k • written 2 days ago by
Lélé
▴ 10
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
2 days ago by
Esraa
• 0
0
votes
0
replies
92
views
ReactomeGSA
ReactomeGSA
2 days ago by
Shaimaa Gamal
▴ 10
0
votes
5
replies
280
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
1
reply
164
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 1 day ago by
DGTool
▴ 20 • written 2 days ago by
iqra
• 0
0
votes
0
replies
98
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dude
• 0
0
votes
0
replies
96
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 days ago by
brunofelicianodeomena
• 0
0
votes
1
reply
146
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
1
vote
2
replies
223
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
1 day ago by
bioinfo
▴ 150
0
votes
2
replies
188
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
2 days ago by
melissa.joubert
• 0
0
votes
0
replies
110
views
Is there a real ground truth for CNV data?
CNV
3 days ago by
jennyp0706
• 0
1
vote
1
reply
145
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 2 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
3
replies
202
views
How to access GWAVA software of data
GWAVA
updated 3 days ago by
GenoMax
142k • written 3 days ago by
nonaddldy
▴ 10
0
votes
0
replies
93
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
176
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
3 days ago by
IdaHao0921
• 0
0
votes
3
replies
343
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
161
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by
lagartija
▴ 160
82 results • Page
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Recent Votes
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
A: Differentially expressed genes between Seurat objects
differential gene expression analysis comparing different conditions using scRNAseq
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
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Popular Question
to
Ezequiel
• 0
Popular Question
to
alanh
▴ 170
Scholar
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Peter
6.0k
Popular Question
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ashkan
▴ 160
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Umer
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Recent Replies
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
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