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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
3
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
1 minute ago by
njornet
▴ 20
0
votes
0
replies
6
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
16 minutes ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
7
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
21 minutes ago by
Lemonhope
• 0
0
votes
0
replies
11
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
30 minutes ago by
Winter
• 0
0
votes
0
replies
22
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
1 hour ago by
Sumeet
• 0
1
vote
1
reply
33
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
2 hours ago by
analyst
▴ 40
0
votes
0
replies
23
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
3 hours ago by
analyst
▴ 40
0
votes
0
replies
45
views
meffil.snp.concordance
meffil
methylation
snp_concordance
8 hours ago by
kyj222637
• 0
0
votes
0
replies
44
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
8 hours ago by
sooni
▴ 20
0
votes
2
replies
81
views
STAR aligner error
RNA-seq
STAR
slurm
10 minutes ago by
M.
▴ 30
0
votes
0
replies
48
views
monocle 3-- Could not get node in small cluster
monocle3
11 hours ago by
synat.keam
▴ 100
0
votes
1
reply
92
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
updated 7 hours ago by
Ram
43k • written 12 hours ago by
Nicholas
• 0
0
votes
3
replies
201
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 13 hours ago by
Ram
43k • written 17 hours ago by
schmince
• 0
0
votes
1
reply
99
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
Sony
▴ 10
5
votes
5
replies
220
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 hours ago by
Chris
▴ 280
0
votes
1
reply
104
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 20 hours ago by
ATpoint
82k • written 20 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
171
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 18 hours ago by
i.sudbery
19k • written 21 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
122
views
student
epitranscriptomics
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
useriwa
• 0
0
votes
0
replies
79
views
Imputation of missing genotypes
panel
beagle
imputation
22 hours ago by
analyst
▴ 40
0
votes
3
replies
139
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 18 hours ago by
GenoMax
142k • written 22 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
71
views
Correlation Analysis
statistics
methylation
NGS
expression
22 hours ago by
Researcher
▴ 30
1
vote
2
replies
146
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
16 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
107
views
Gene density plot
density
gene
updated 17 hours ago by
dthorbur
★ 1.9k • written 23 hours ago by
gubrins
▴ 290
0
votes
0
replies
92
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
95
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
103
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
92
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
418
views
Question regarding WGCNA
WGCNA
Network-construction
updated 18 hours ago by
andres.firrincieli
3.6k • written 4 days ago by
deepak
• 0
0
votes
0
replies
99
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
0
votes
1
reply
176
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 21 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
108
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 1 day ago by
Ram
43k • written 1 day ago by
sidrah.maryam
▴ 50
0
votes
0
replies
96
views
Normalizing AMR gene count data
abundance
RGI
updated 1 day ago by
Ram
43k • written 1 day ago by
arshad1292
▴ 100
0
votes
0
replies
107
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
sarumonsus
• 0
0
votes
0
replies
112
views
How to implement an IGV to streamlit app?
python
streamlit
igv
2 days ago by
avigail.shnaider
• 0
0
votes
0
replies
121
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
111
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
2 days ago by
Christopher
• 0
0
votes
0
replies
114
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
0
votes
0
replies
122
views
Seurat V5 integration
Seurat
samples
integration
combine
2 days ago by
starswillfade
▴ 10
0
votes
1
reply
180
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 1 day ago by
bk11
★ 2.4k • written 3 days ago by
Yoosef
▴ 60
0
votes
1
reply
256
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
0
votes
1
reply
211
views
Help with DGEList function
DGEList
R
updated 2 days ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
0
replies
150
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
1
reply
197
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Ximena
• 0
0
votes
1
reply
190
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 4 days ago by
Ram
43k • written 4 days ago by
Valentina
• 0
0
votes
6
replies
417
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 4 days ago by
swbarnes2
14k • written 4 days ago by
Erina
• 0
1
vote
3
replies
277
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
2 days ago by
Lada
▴ 30
1
vote
0
replies
145
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 2 days ago by
zx8754
11k • written 4 days ago by
Emilie
▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
4 days ago by
Javier
• 0
0
votes
1
reply
231
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 4 days ago by
Thanujay S
• 0 • written 4 days ago by
yahn
• 0
0
votes
0
replies
130
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
4 days ago by
mikemakaveli1
• 0
1,000 results • Page
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Recent Votes
Comment: java out of memory error through beagle for imutation
Analysis of intronic reads included scRNA-seq data
removeBatchEffect explained using base R linear models
Answer: ChIP-seq datasets: input samples omitted?
Answer: ChIP-seq datasets: input samples omitted?
Answer: Is therer any suggestions on mapping rate of WGBS data?
A: Download full list of SNPs and their coordinates in hg38
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Recent Replies
Comment: STAR aligner error
by
M.
▴ 30
I already told them but they couldn't come up with a useful solution :/
Comment: A question about reference genome for creating the consensus sequence
by
ATpoint
82k
You aligned your data, that is your reference genome to compare against. If you want to change reference then realign.
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The vignette I followed, although lacking, seems better since it focuses on doing iterative process. I'll keep looking perhaps I'll find so…
Comment: A question about reference genome for creating the consensus sequence
by
me
• 0
Hi, yes, my cram files cover the whole genome, which is actually individual genome information. I wonder how to adjust the base genome. Tha…
Comment: CNVKIT - unable to produce scatter and diagram pdfs
by
DGTool
• 0
At least according to the documentation, it seems for WGS you can use the `batch --method wgs` option. There is more information here: [htt…
Answer: A question about reference genome for creating the consensus sequence
by
ATpoint
82k
It is the consensus for all reads that overlap a given base, it's not a genome consensus unless your reads cover the entire genome.
Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
Hello everyone, I need to call the CNV from my hunam WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am tr…
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 30
I don't think dropout is playing an important role with Malat1 since it is usually highly expressed. On the other hand, if dropout is still…
Comment: java out of memory error through beagle for imutation
by
analyst
▴ 40
Resolved by increasing heapsize of -Xmx50G
Comment: STAR aligner error
by
Ram
43k
Talk to your HPC sysadmin - array jobs might be getting different kinds of nodes compared to standalone jobs.
Comment: Is therer any suggestions on mapping rate of WGBS data?
by
Zeng Jingyu
▴ 60
Thank you for your answer!
Answer: HCL database download
by
sooni
▴ 20
I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing
by
mizraelson
▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
qwertyuiop26
• 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
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