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113,891 results • Page
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Bioinformatics
question
Bioinformatics
just now by
Daniel
• 0
0
votes
0
replies
5
views
bootstraped treemix show no migration event
Treemix
Bootstrap
20 minutes ago by
reza
▴ 300
0
votes
1
reply
96
views
Are 10x cellranger-arc ATAC bam files deduplicated?
singlecell
10x
updated 3 hours ago by
swbarnes2
13k • written 16 hours ago by
WaterMetal
• 0
0
votes
4
replies
165
views
From TPM to raw counts
tpm
Deconvolution
rnaseq
1 hour ago by
Gama313
▴ 120
0
votes
2
replies
119
views
Low coverage whole genome sequencing reveal excess heterozygosity for multiple SNPs. How to filter?
lcWGS
WGS
heterozygosity
5 hours ago by
beausoleilmo
▴ 560
3
votes
3
replies
312
views
How to obtain data on the coordinates of the Exon region from UCSC
hg19
UCSC
exon
6 hours ago by
ayasu
• 0
772
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
2
votes
4
replies
176
views
Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes
contamination
metagenomics
updated 5 hours ago by
Mensur Dlakic
★ 25k • written 12 hours ago by
btc347
• 0
0
votes
2
replies
1.4k
views
Does GNOMAD use all LOFTEE LoF filters?
loftee
gnomad
LOF
ensembl
vep
updated 8 hours ago by
AMARU
• 0 • written 3.8 years ago by
brismiller
▴ 50
0
votes
3
replies
712
views
"MethylKit" package for WGBS data
MethylKit
WGBS
updated 9 hours ago by
viveksomya123
• 0 • written 2.3 years ago by
shrinka.genetics
▴ 20
4
votes
3
replies
238
views
GO categorization
Ontology
Gene
updated 12 hours ago by
geneontologyhelp
▴ 290 • written 1 day ago by
m.habib
• 0
0
votes
0
replies
62
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
13 hours ago by
James
• 0
0
votes
0
replies
58
views
Job:
Postdoc in comparative genomics of plant-associated bacteria (Polytechnic University of Madrid, SPAIN)
evolution
genomics
mutation
bacteria
genomes
13 hours ago by
Alejandro
• 0
0
votes
1
reply
298
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
updated 14 hours ago by
Jordan M Eizenga
▴ 410 • written 7 days ago by
Wenke
• 0
0
votes
1
reply
170
views
How to find node Postion and source(sample) ?
vg
updated 14 hours ago by
Jordan M Eizenga
▴ 410 • written 3 days ago by
zhang yi xing
▴ 20
0
votes
0
replies
67
views
Job:
Assistant Professor: Molecular Biology
Biology
Molecular
UCSD
14 hours ago by
lta
▴ 10
0
votes
0
replies
53
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
14 hours ago by
Mehwish
▴ 10
0
votes
0
replies
72
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs
promoters
bioinformatics
15 hours ago by
shome
▴ 10
1
vote
1
reply
110
views
Finding human .vcf files online to download
human
findvcf
vcf
updated 15 hours ago by
cmdcolin
★ 3.4k • written 16 hours ago by
eren.idil
▴ 10
0
votes
0
replies
54
views
Issue with genetic QC sex check
plink
15 hours ago by
kl
▴ 10
0
votes
2
replies
150
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
4 hours ago by
fluke
• 0
1
vote
3
replies
164
views
How Can I move the scattered dots more closer into the center of box ?
R
Boxplots
geom_jitter
updated 7 hours ago by
GenoMax
136k • written 18 hours ago by
ohtang7
▴ 40
0
votes
1
reply
111
views
How to identify CG, CHG, or CHH from MeDIP data
MethylationStudy
CHG
CHH
CG
MeDIP
14 hours ago by
Tm
★ 1.1k
0
votes
0
replies
79
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
20 hours ago by
CoLa
• 0
0
votes
0
replies
88
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
21 hours ago by
ManuelDB
▴ 80
11
votes
6
replies
333
views
Problematic fastq files...How can we trust them?
fastq
12 hours ago by
blackadder
▴ 30
1
vote
3
replies
185
views
An incomprehensible error with R package gggenes
R
gggenes
visualize
updated 22 hours ago by
ATpoint
78k • written 23 hours ago by
alice005201314
• 0
3
votes
2
replies
201
views
Should I scale all genes in single cell Seurat?
singlecell
10 hours ago by
synat.keam
▴ 80
0
votes
1
reply
127
views
doubt about usage of megahit
trinity
megahit
updated 19 hours ago by
Istvan Albert
99k • written 1 day ago by
meera
• 0
0
votes
0
replies
77
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
1 day ago by
Peerzada
• 0
0
votes
1
reply
133
views
DIAMOND tutorial
tutorial
DIAMOND
updated 1 day ago by
GenoMax
136k • written 1 day ago by
sooni
▴ 10
0
votes
13
replies
922
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling
chromium
cellranger
scFFPE
updated 1 day ago by
MohammadAlkadi
▴ 70 • written 6 weeks ago by
bk11
★ 1.8k
0
votes
2
replies
219
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic
bioinformatic
updated 1 day ago by
Kevin Blighe
86k • written 1 day ago by
Giovana
• 0
2
votes
8
replies
685
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 1 day ago by
ATpoint
78k • written 19 days ago by
ellen.francis
▴ 10
0
votes
0
replies
100
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
1 day ago by
O.rka
▴ 710
0
votes
1
reply
395
views
Loftee no splice site annotations
Loftee
VEP
updated 1 day ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
1
vote
1
reply
171
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq
bulk_RNA-seq
online_course
updated 1 day ago by
swbarnes2
13k • written 1 day ago by
ire
• 0
0
votes
1
reply
125
views
gene set enrichment analysis- by enrichGO
rna-seq
GO
enrichment
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
CL
• 0
0
votes
0
replies
86
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
1 day ago by
luckyday1661
• 0
0
votes
1
reply
129
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Nicolas
• 0
0
votes
0
replies
104
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
1 day ago by
Ty
• 0
0
votes
1
reply
153
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
updated 22 hours ago by
cmdcolin
★ 3.4k • written 1 day ago by
Trevor
• 0
0
votes
0
replies
103
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
1 day ago by
bioinfo
▴ 140
0
votes
1
reply
161
views
Where do these snpeff annotation come from?
snpeff
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
curious
▴ 730
4
votes
4
replies
282
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
1 day ago by
CTLong
▴ 20
4
votes
5
replies
877
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 1 day ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
0
votes
3
replies
220
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
Jingfang
• 0
3
votes
2
replies
458
views
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
SNP
bbtools
updated 1 day ago by
harold.smith.tarheel
★ 4.9k • written 1 day ago by
Axzd
▴ 50
0
votes
1
reply
112
views
News:
Course: Genome Assembly and Annotation
GenomeAssembly
GenomeAnnotation
Longreads
Bioinformatics
Biodiversity
updated 1 day ago by
sil_bioinfo
▴ 30 • written 1 day ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
238
views
How I add new organism "Beauveria bassiana (strain ARSEF 2860)" in ClueGo plug-in of cytoscape?
cytoscape
updated 1 day ago by
Scooter
▴ 180 • written 26 days ago by
A
• 0
113,891 results • Page
1 of 2278
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
GenoMax
136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts
by
Gama313
▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
by
swbarnes2
13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
fluke
• 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts
by
Istvan Albert
99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
beausoleilmo
▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo
by
CTLong
▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC
by
ayasu
• 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts
by
Brian Bushnell
19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in
by
Mensur Dlakic
★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S
by
Brian Bushnell
19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters?
by
AMARU
• 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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