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544 results • Page
1 of 11
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Votes
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0
votes
0
replies
28
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
how-to
1 hour ago by
glaciya2018
• 0
0
votes
0
replies
38
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
3 hours ago by
pramach1
▴ 40
0
votes
1
reply
51
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 hour ago by
Sofia
• 0 • written 5 hours ago by
mawigoj318
• 0
0
votes
0
replies
59
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
7 hours ago by
salias
• 0
0
votes
2
replies
109
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated 3 hours ago by
Istvan Albert
100k • written 7 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
48
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
single-cell
suppa
rnaseq
splicing
alternative
2 hours ago by
newuser2024
• 0
0
votes
0
replies
42
views
Network Alignment
plugin
Cytoscape
CytoMCS
8 hours ago by
Akash D
▴ 40
0
votes
1
reply
83
views
alignment result
RNA-seq
samtool
analysis
hisat2
updated 5 hours ago by
GenoMax
141k • written 9 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
47
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
hetero
Seurat
modelHomotypic
DoubletFinder
10 hours ago by
Jeyong
• 0
0
votes
1
reply
93
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 hours ago by
jkim
▴ 170 • written 12 hours ago by
Aaliya
• 0
0
votes
0
replies
62
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
17 hours ago by
Kash
▴ 110
0
votes
1
reply
101
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 13 hours ago by
Mensur Dlakic
★ 27k • written 19 hours ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
177
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 8 hours ago by
b.contreras.moreira
▴ 170 • written 19 hours ago by
v.berriosfarias
▴ 140
2
votes
9
replies
771
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 16 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
337
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
13 hours ago by
atowns21
• 0
0
votes
1
reply
113
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 21 hours ago by
bk11
★ 2.3k • written 22 hours ago by
alphaflylizard
• 0
0
votes
0
replies
72
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
0
votes
1
reply
128
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
0
votes
5
replies
250
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
5 hours ago by
njornet
▴ 20
0
votes
0
replies
74
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 1 day ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
0
replies
86
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
1
vote
3
replies
186
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
1
vote
3
replies
222
views
some error in building kraken2 database
metagenome
kraken2
15 hours ago by
Art1ess
• 0
0
votes
1
reply
117
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
1
vote
1
reply
148
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
1
reply
182
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 18 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
77
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 day ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
1
reply
131
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
268
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
0
votes
0
replies
101
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
0
votes
0
replies
84
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 1 day ago by
Ram
43k • written 1 day ago by
sansan_96
▴ 80
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
0
replies
132
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
236
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
0
votes
1
reply
119
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
2
replies
175
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
2
replies
141
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
114
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
0
votes
0
replies
79
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
0
votes
0
replies
69
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
2
votes
4
replies
229
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
8 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
75
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
1
reply
137
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
0
votes
0
replies
67
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
0
votes
0
replies
83
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
0
votes
0
replies
68
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
0
votes
0
replies
75
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
0
votes
0
replies
118
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
544 results • Page
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Recent Replies
Comment: AGeNT LocatIt
by
barslmn
★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates
by
Sofia
• 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt
by
Greg
• 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed)
by
jkim
▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
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