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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
5
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
6 minutes ago by
Sumeet
• 0
0
votes
1
reply
17
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
58 minutes ago by
analyst
▴ 30
0
votes
0
replies
11
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
1 hour ago by
analyst
▴ 30
0
votes
0
replies
40
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
5 hours ago by
me
• 0
0
votes
0
replies
42
views
meffil.snp.concordance
meffil
methylation
snp_concordance
6 hours ago by
kyj222637
• 0
0
votes
0
replies
40
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
7 hours ago by
sooni
▴ 20
0
votes
1
reply
69
views
STAR aligner error
RNA-seq
STAR
slurm
updated 2 hours ago by
Ram
43k • written 9 hours ago by
M.
▴ 30
0
votes
0
replies
46
views
monocle 3-- Could not get node in small cluster
monocle3
9 hours ago by
synat.keam
▴ 100
0
votes
1
reply
88
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
updated 5 hours ago by
Ram
43k • written 10 hours ago by
Nicholas
• 0
0
votes
3
replies
193
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 11 hours ago by
Ram
43k • written 15 hours ago by
schmince
• 0
0
votes
1
reply
95
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
Sony
▴ 10
5
votes
5
replies
218
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
4 hours ago by
Chris
▴ 280
0
votes
1
reply
103
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 18 hours ago by
ATpoint
82k • written 19 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
169
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 16 hours ago by
i.sudbery
19k • written 19 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
119
views
student
epitranscriptomics
updated 19 hours ago by
ATpoint
82k • written 20 hours ago by
useriwa
• 0
0
votes
0
replies
77
views
Imputation of missing genotypes
panel
beagle
imputation
20 hours ago by
analyst
▴ 30
0
votes
3
replies
137
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 17 hours ago by
GenoMax
142k • written 20 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
69
views
Correlation Analysis
statistics
methylation
NGS
expression
21 hours ago by
Researcher
▴ 30
1
vote
2
replies
145
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
15 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
105
views
Gene density plot
density
gene
updated 16 hours ago by
dthorbur
★ 1.9k • written 22 hours ago by
gubrins
▴ 290
1
vote
4
replies
223
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
9 hours ago by
qwertyuiop26
• 0
0
votes
0
replies
90
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
92
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
99
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
89
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
417
views
Question regarding WGCNA
WGCNA
Network-construction
updated 16 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
173
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 20 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
106
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
94
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 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
sarumonsus
• 0
0
votes
0
replies
111
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
0
votes
0
replies
120
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
178
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
210
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
276
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 1 day 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
129
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
2
votes
2
replies
215
views
Raw counts using stringtie
stringtie
RNA-seq
updated 4 days ago by
GenoMax
142k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
129
views
Modify plot R mtDNA indel
plot
mtDNA
R
4 days ago by
marco.barr
▴ 90
1,000 results • Page
1 of 20
Recent Votes
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
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
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★ 16k
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Recent Replies
Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
Hello everyone, I need to call the CNV from my WGS data. I searched for many tutorial, but I did'nt get any proper procedure. I am trying t…
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
▴ 30
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 …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
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