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19 results • Page
1 of 1
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Views
Votes
Replies
0
votes
0
replies
14
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
55 minutes ago by
avocado123
• 0
0
votes
0
replies
13
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
1 hour ago by
Emily
▴ 10
0
votes
0
replies
18
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 hour ago by
rohitsatyam102
▴ 840
0
votes
0
replies
18
views
how to read graph_test output of monocle 3
monocle3
1 hour ago by
synat.keam
▴ 100
0
votes
1
reply
354
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 2 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
52
views
BLAST using both nucleotides and taxonomic local databases
blast
ncbi
taxid
taxonomy
6 hours ago by
Begonia_pavonina
▴ 150
2
votes
3
replies
112
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
updated 2 hours ago by
Pierre Lindenbaum
161k • written 7 hours ago by
QX
• 0
0
votes
0
replies
49
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
8 hours ago by
Aspire
▴ 300
0
votes
2
replies
128
views
Highest variable features in single cell data
cell
single
7 hours ago by
Kazo
• 0
0
votes
1
reply
106
views
PCA plot
DESeq2
PCAplot
updated 3 hours ago by
jkim
▴ 170 • written 14 hours ago by
Aaliya
▴ 10
0
votes
0
replies
77
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
17 hours ago by
4fzcgueyp5
• 0
0
votes
1
reply
130
views
Annovar using R package
Annovar
gnomAD
R
updated 19 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
DKA
▴ 40
0
votes
5
replies
246
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 4 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
103
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 22 hours ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
4
replies
227
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
9 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
93
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 22 hours ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
173
views
alignment result
RNA-seq
samtools
hisat2
12 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
85
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 22 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
2
replies
225
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 22 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
19 results • Page
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Recent Votes
Answer: How do I get the 3bp sequence on either side of a co-ordinate
What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 840
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
Comment: GAPIT p-value significance threshold
by
ginellegrenier
• 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot
by
jkim
▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
Comment: ScRNA data question
by
bk11
★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
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