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444 results • Page
3 of 9
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Votes
Replies
0
votes
0
replies
161
views
how to read graph_test output of monocle 3
monocle3
10 days ago by
synat.keam
▴ 100
0
votes
1
reply
511
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 10 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
0
replies
160
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
10 days ago by
Aspire
▴ 330
0
votes
3
replies
325
views
Highest variable features in single cell data
single-cell
updated 8 days ago by
bk11
★ 2.4k • written 10 days ago by
carolofharvest
▴ 30
1
vote
3
replies
395
views
PCA plot
DESeq2
PCAplot
updated 6 days ago by
LauferVA
4.2k • written 10 days ago by
Aaliya
▴ 10
0
votes
0
replies
157
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
10 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
283
views
Annovar using R package
Annovar
gnomAD
R
9 days ago by
DKA
▴ 40
0
votes
5
replies
388
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 10 days ago by
GenoMax
142k • written 11 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
152
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 10 days ago by
Ram
43k • written 11 days ago by
glaciya2018
• 0
0
votes
0
replies
314
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
11 days ago by
pramach1
▴ 40
0
votes
1
reply
178
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 11 days ago by
Sofia
• 0 • written 11 days ago by
mawigoj318
• 0
0
votes
0
replies
152
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
11 days ago by
salias
• 0
0
votes
5
replies
386
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 8 days ago by
Istvan Albert
100k • written 11 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
130
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 10 days ago by
Ram
43k • written 11 days ago by
newuser2024
• 0
1
vote
2
replies
257
views
alignment result
RNA-seq
samtools
hisat2
10 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
122
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
11 days ago by
Kash
▴ 110
0
votes
1
reply
170
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 11 days ago by
Mensur Dlakic
★ 27k • written 11 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
306
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 10 days ago by
Ram
43k • written 11 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
896
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 11 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
626
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
9 days ago by
atowns21
• 0
0
votes
1
reply
187
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 11 days ago by
bk11
★ 2.4k • written 11 days ago by
alphaflylizard
• 0
0
votes
0
replies
108
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
12 days ago by
ohtang7
▴ 40
0
votes
1
reply
185
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Srinka
▴ 20
0
votes
5
replies
375
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
11 days ago by
njornet
▴ 20
0
votes
0
replies
107
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 12 days ago by
Ram
43k • written 12 days ago by
SHREYA
• 0
0
votes
0
replies
112
views
Merging replicates from Encode project
CHIP-seq
encode
12 days ago by
Nurken
• 0
1
vote
3
replies
267
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
12 days ago by
WouterDeCoster
47k
1
vote
3
replies
304
views
some error in building kraken2 database
metagenome
kraken2
11 days ago by
Art1ess
• 0
0
votes
1
reply
183
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 12 days ago by
bk11
★ 2.4k • written 12 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
195
views
Failed kmer content
kmer
illumina
ngs
updated 12 days ago by
Ram
43k • written 12 days ago by
Kasturi
• 0
0
votes
0
replies
101
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 12 days ago by
Ram
43k • written 12 days ago by
SSSJec
• 0
0
votes
1
reply
163
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 12 days ago by
Ram
43k • written 12 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
397
views
Error in cnetplot enrichplot package
R
updated 12 days ago by
Ram
43k • written 12 days ago by
Farhad
• 0
0
votes
0
replies
118
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 12 days ago by
Ram
43k • written 12 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
104
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 12 days ago by
Ram
43k • written 12 days ago by
sansan_96
▴ 80
0
votes
0
replies
107
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 12 days ago by
Ram
43k • written 12 days ago by
Amélie
• 0
0
votes
0
replies
212
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 12 days ago by
Ram
43k • written 12 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 12 days ago by
chrchang523
10k • written 6.2 years ago by
Ginevra
▴ 10
1
vote
8
replies
476
views
Downsampling fastq file
downsample
fastq
4 days ago by
marco.barr
▴ 90
0
votes
1
reply
150
views
tbtool
tbtool
updated 13 days ago by
Ram
43k • written 13 days ago by
Raman
• 0
0
votes
10
replies
524
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 5 days ago by
i.sudbery
19k • written 13 days ago by
Patadu94
• 0
0
votes
1
reply
141
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 13 days ago by
ATpoint
82k • written 13 days ago by
enanoide
• 0
0
votes
0
replies
97
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
13 days ago by
manaswwm
▴ 510
0
votes
0
replies
85
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
12 days ago by
alifafiq1
• 0
0
votes
0
replies
92
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
13 days ago by
feather-W
• 0
2
votes
4
replies
334
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
11 days ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
92
views
Annotating single cell data automatically
cell
annotation
single
13 days ago by
Gerard
• 0
0
votes
1
reply
178
views
RNA-seq bacteria contamination
RNA-seq
updated 13 days ago by
GenoMax
142k • written 13 days ago by
sh
• 0
0
votes
0
replies
84
views
Imputation advice
imputation
13 days ago by
kl
▴ 10
0
votes
0
replies
105
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
13 days ago by
Enrique
• 0
444 results • Page
3 of 9
Recent Votes
Comment: agilent human all exon sureselct v7 bed file
Answer: install package
Comment: Overlap File for RACON Genome Polisher
Overlap File for RACON Genome Polisher
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
Answer: LD-prune variants while maintaining a list of SNPs
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Recent Replies
Comment: agilent human all exon sureselct v7 bed file
by
MiladAD
▴ 10
God bless you man.
Answer: install package
by
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▴ 40
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
Lada
▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
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I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
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• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
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Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
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Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
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Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
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Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
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