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711 results • Page
4 of 15
Sort: replies
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Views
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Replies
2
votes
5
replies
966
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 23 days ago by
Wayne
★ 2.0k • written 2.1 years ago by
arinjoy
• 0
0
votes
5
replies
368
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
14 days ago by
me
• 0
5
votes
5
replies
693
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 19 days ago by
Mbofire
• 0 • written 28 days ago by
Ming Tommy Tang
★ 3.9k
3
votes
5
replies
471
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
1 day ago by
beantkapoor16
▴ 10
4
votes
5
replies
3.5k
views
How to compare compare two Sam files to check mapping
alignment
updated 14 days ago by
DavidStreid
▴ 90 • written 6.4 years ago by
madhu.9124
▴ 60
2
votes
4
replies
419
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 29 days ago by
swbarnes2
14k • written 4 weeks ago by
dxj294
• 0
0
votes
4
replies
227
views
Where to find old version of GATK best practice
gatk
1 day ago by
Zhenyu Zhang
★ 1.2k
0
votes
4
replies
319
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
1 day ago by
Luqman
• 0
0
votes
4
replies
438
views
Highest variable features in single cell data
single-cell
15 days ago by
carolofharvest
▴ 40
0
votes
4
replies
329
views
Genbank File Format
gbkformat
23 days ago by
alenew.am
• 0
0
votes
4
replies
270
views
Sequencing Depth (Read Depth) Calculations
depth
7 days ago by
LucisTheFather
• 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq
alignment
RNA-Seq
featureCounts
STAR
updated 9 days ago by
Thind amarinder
▴ 340 • written 5.0 years ago by
garbuzov
▴ 70
0
votes
4
replies
360
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 23 days ago by
Ram
44k • written 23 days ago by
Hamtaro
▴ 50
1
vote
4
replies
372
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 9 days ago by
Ram
44k • written 14 days ago by
samRayne
• 0
1
vote
4
replies
428
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
15 days ago by
heelpPlease
• 0
2
votes
4
replies
362
views
from row count to tpm
tpm
row-count
normalization
updated 22 days ago by
Ram
44k • written 4 weeks ago by
michelafrancesconi9
▴ 20
2
votes
4
replies
302
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 7 days ago by
yura.grabovska
▴ 90 • written 7 days ago by
ev97
▴ 20
1
vote
4
replies
321
views
Add stats to boxplot in R
stats
R
7 days ago by
Ghada
• 0
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 14 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
2
votes
4
replies
398
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
29 days ago by
samuelkalandarov2002
▴ 10
1
vote
4
replies
430
views
Segmentation error while using a tool
smalt
updated 18 days ago by
Mensur Dlakic
★ 27k • written 19 days ago by
Ruqaiya
• 0
6
votes
4
replies
384
views
Details on salmon index
Salmon
updated 5 days ago by
Rob
6.6k • written 7 days ago by
Lorenzo
• 0
0
votes
4
replies
172
views
merge overlaps and remove non overlap genomic windows
BED
intersection
overlap
12 hours ago by
reza
▴ 300
2
votes
4
replies
248
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
12 hours ago by
Arton
▴ 10
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
20 days ago by
eebloom
▴ 80
0
votes
4
replies
342
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
3 days ago by
Bibi
• 0
3
votes
4
replies
360
views
Truncated metadata file report from ENA Portal API
ena
python
12 days ago by
Giulia
• 0
0
votes
4
replies
42
views
Z score
Z
score
just now by
Akash D
▴ 40
0
votes
4
replies
339
views
Correlation Analysis
statistics
methylation
NGS
expression
12 days ago by
Researcher
▴ 30
3
votes
4
replies
433
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
27 days ago by
QX
• 0
0
votes
4
replies
216
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
1 day ago by
shpak.max
▴ 50
1
vote
4
replies
530
views
cellranger error message
multiplexing
cellranger
updated 12 days ago by
Max
• 0 • written 3 months ago by
Alivia
▴ 10
0
votes
4
replies
420
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
10 days ago by
beginner123
• 0
0
votes
4
replies
277
views
Galaxy StringTie error
stringtie
galaxy
8 days ago by
trkfs
• 0
1
vote
4
replies
298
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 2 days ago by
Ram
44k • written 2 days ago by
Harshita
• 0
2
votes
4
replies
2.5k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 28 days ago by
ZhangYuanfeng
• 0 • written 2.5 years ago by
Frazier Baker
• 0
5
votes
4
replies
745
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
29 days ago by
kirillkirilenko
▴ 40
3
votes
4
replies
499
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 16 days ago by
Gordon Smyth
★ 7.2k • written 19 days ago by
SHN
▴ 40
1
vote
4
replies
443
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 12 days ago by
GenoMax
142k • written 5 weeks ago by
aniigodwinn
• 0
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 28 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
3
votes
4
replies
439
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 6 days ago by
GenoMax
142k • written 7 days ago by
Pierre Lindenbaum
162k
2
votes
4
replies
728
views
Count all variants from vcf file
variants
vcf
Count
updated 16 days ago by
Pierre Lindenbaum
162k • written 21 months ago by
t.ali
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 9 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 8 days ago by
Ram
44k • written 13 months ago by
mohyeddine.taleb
• 0
1
vote
4
replies
357
views
some error in building kraken2 database
metagenome
kraken2
updated 31 minutes ago by
ahmet
• 0 • written 29 days ago by
Art1ess
• 0
2
votes
4
replies
441
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
29 days ago by
HyperEvo
• 0
2
votes
4
replies
298
views
Where to get the following bed file?
WES
bed
reference
file
updated 16 days ago by
GenoMax
142k • written 16 days ago by
wyuan37
• 0
1
vote
4
replies
508
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 29 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
2
votes
4
replies
322
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
8 days ago by
Esraa
• 0
0
votes
4
replies
368
views
Merge clusters in Seurat UMAP
seurat
umap
6 days ago by
kilcdincer
▴ 10
711 results • Page
4 of 15
Recent Votes
A: Fold change - a final explanation
Comment: scRNA-seq quality control
Comment: How to get the ratio of allele counts from GATK derived VCF file?
Setting up Aspera Connect (ascp) on Linux and macOS
Setting up Aspera Connect (ascp) on Linux and macOS
Answer: Genes' fpkm values through cufflink
Answer: Genes' fpkm values through cufflink
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ATpoint
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Recent Replies
Comment: Z score
by
Akash D
▴ 40
Alright! Got you...
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
It very much depends on whether the OP does want/need to do the CellRanger runs locally or not. Doesn't really matter if its only occasion…
Comment: log2 fold change in RNA-seq analysis
by
Mensur Dlakic
★ 27k
Everything is already explained on this page, just read everything already written above. Specifically, [**this comment**][1]. [1]: htt…
Answer: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Answer: GWAS Phenotypes
by
韩雨
• 0
In my opinion, the basis of the question is to solve whether the phenotype is regulated by genetics. In the aspect of genetic, the estima…
Answer: Classic threshold for log2 fold change in RNA-seq experiment
by
May Ling
• 0
Good day everyone, Sorry I found a bit confusing and would appreciate if I could clarify on the calculation. I am using DESeq. My desire…
Comment: some error in building kraken2 database
by
ahmet
• 0
Were you able to fix this issue? I'm also trying to add external species to krakendb
Comment: Z score
by
ATpoint
82k
logFCs are a bit difficult to cluster I think, because fold changes without stats attached to it are meaningless. They can be very big, due…
Comment: Z score
by
Akash D
▴ 40
Ok. However, if i perform it on log2FC, there wont be any control samples visible in my heatmap. Your answer is perfect.
Comment: Z score
by
ATpoint
82k
You can apply Z-scores on whatever you want, but it must make sense and depends on what you want to do. What is the context? See for exampl…
Answer: Z score in RNAseq
by
Akash D
▴ 40
Can Z score be applied on log2FC and then visualized? Alternatively, Can log2FC be converted to Z scores and then visualized as heatmap?
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Just for comparison, I deal with scRNA-seq daily and my workstation is a 12700k i7 with 128GB RAM and even this is actually more than I nee…
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
by
colindaven
6.4k
- As others have said, 1-2 workstations are probably the way to go. - A Linux OS like Ubuntu is probably easiest and has best docs - RA…
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
anikcropscience
▴ 230
Ok, thank you for the reply. I will check out the DP field then.
Comment: Alternatives To Liftover
by
Thanujay S
• 0
Hey! Would you consider building an API for the same? Is that something you have planned?
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