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735 results • Page
1 of 15
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0
votes
0
replies
9
views
Does it possible to know what are the adjacent genes up to 1000bp upstream and downstream of IS element
Transposons
30 minutes ago by
Neel
▴ 10
0
votes
0
replies
39
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
4 hours ago by
rheab1230
▴ 140
0
votes
1
reply
77
views
Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data
splicing
RNA-seq
updated 2 hours ago by
iraun
5.8k • written 7 hours ago by
ntsopoul
▴ 20
0
votes
2
replies
109
views
Creating loop for read groups using Picard
bash
picard
loop
updated 4 hours ago by
ntsopoul
▴ 20 • written 8 hours ago by
brandnewatthis
• 0
0
votes
1
reply
81
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 7 hours ago by
Mensur Dlakic
★ 23k • written 8 hours ago by
Sian
• 0
1
vote
0
replies
81
views
Creating sample groups from a combination of genes for survival analysis
Survival
8 hours ago by
krushnach80
★ 1.1k
3
votes
2
replies
124
views
Power analysis for patient samples
RNA-seq
12 hours ago by
aropri
▴ 130
0
votes
0
replies
69
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
14 hours ago by
HERMAN
▴ 10
0
votes
0
replies
58
views
Error when using compareCluster from enichment
compareCluster
14 hours ago by
jacob
• 0
0
votes
0
replies
75
views
Need Help Scraping MeSH terms from Pubmed
Python
Entrez
Scraping
updated 13 hours ago by
Ram
38k • written 14 hours ago by
Arnau
• 0
1
vote
1
reply
97
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 14 hours ago by
GenoMax
127k • written 14 hours ago by
emmanouil.a
▴ 110
0
votes
2
replies
127
views
How to add gene information below the BSmooth result ?
BSmooth
methylation
DNA
8 hours ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
112
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 15 hours ago by
Basti
★ 1.4k • written 15 hours ago by
flourde
• 0
1
vote
5
replies
266
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 11 hours ago by
Trivas
▴ 660 • written 19 hours ago by
TJay
• 0
0
votes
1
reply
104
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 17 hours ago by
Pierre Lindenbaum
153k • written 17 hours ago by
rj.rezwan
• 0
0
votes
0
replies
81
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
18 hours ago by
zhangfish
▴ 40
0
votes
0
replies
69
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
18 hours ago by
Joana
• 0
0
votes
0
replies
105
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
18 hours ago by
firestar
★ 1.5k
0
votes
0
replies
89
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
19 hours ago by
predeus
★ 1.8k
0
votes
0
replies
91
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
19 hours ago by
ucbtep
▴ 20
2
votes
5
replies
205
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 19 hours ago by
Pierre Lindenbaum
153k • written 21 hours ago by
Sarah
▴ 30
0
votes
0
replies
118
views
Dnaplotter
Artemis
22 hours ago by
prs
• 0
1
vote
1
reply
164
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 21 hours ago by
Basti
★ 1.4k • written 23 hours ago by
Stefanus C.B.
• 0
0
votes
1
reply
152
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 1 day ago by
Mensur Dlakic
★ 23k • written 1 day ago by
dgrace999
• 0
0
votes
0
replies
118
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
1 day ago by
melissachuaphd
• 0
0
votes
0
replies
109
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
1 day ago by
William
▴ 10
0
votes
0
replies
137
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
1 day ago by
Tadeoye
▴ 30
0
votes
0
replies
118
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
1 day ago by
eager_underdog
• 0
0
votes
5
replies
292
views
How can I determine the number of detected genes and detected transcripts/isoforms in a BAM file + GTF file?
rnaseq
scRNA-seq
single-cell
genomics
ngs
updated 18 hours ago by
GenoMax
127k • written 1 day ago by
O.rka
▴ 650
0
votes
2
replies
185
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 1 day ago by
Ram
38k • written 1 day ago by
bobbybobbobbo
• 0
1
vote
3
replies
246
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 1 day ago by
GenoMax
127k • written 1 day ago by
Pegasus
▴ 80
0
votes
1
reply
161
views
Circos plot
circos
updated 21 hours ago by
Fabio Marroni
★ 3.0k • written 1 day ago by
prs
• 0
0
votes
1
reply
115
views
mpileup2sync
mpileup2sync
population2
updated 1 day ago by
Ram
38k • written 1 day ago by
Hayler Edu
▴ 30
0
votes
0
replies
86
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 1 day ago by
Ram
38k • written 1 day ago by
Jesús M
• 0
0
votes
2
replies
143
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
1 day ago by
barbarainb
• 0
0
votes
0
replies
71
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
1 day ago by
Roy
▴ 10
0
votes
0
replies
94
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
1 day ago by
ghataksnd
▴ 10
0
votes
0
replies
105
views
samtools mpileup - bases string explanation
samtools
mpileup
1 day ago by
igorm
▴ 20
0
votes
3
replies
222
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 1 day ago by
Ram
38k • written 1 day ago by
VANSHIKA
• 0
0
votes
2
replies
173
views
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
vcf.gz
UnicodeDecodeError
ancIBD
1 day ago by
wangjincheng
• 0
0
votes
1
reply
192
views
Error while running Virusfinder
Virusfinder
updated 1 day ago by
Ram
38k • written 1 day ago by
DC
• 0
0
votes
0
replies
138
views
Fine mapping with GWAS
PAINTOR
GWAS
FINE-MAP
POST-GWAS
updated 1 day ago by
Nicolas Rosewick
10k • written 1 day ago by
Swati
• 0
0
votes
0
replies
126
views
How would I assess evolutionary estimates between duplicated vs. non-duplicated genes in PAML?
PAML
2 days ago by
codoncity
• 0
1
vote
3
replies
278
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 21 hours ago by
Basti
★ 1.4k • written 2 days ago by
Pegasus
▴ 80
1
vote
2
replies
237
views
Handling single-sample VCF after haplotypecaller
VCF
2 days ago by
Y.H.P
• 0
0
votes
0
replies
141
views
MethylR on bam files Gives Error
MethylR
bismark
2 days ago by
anasjamshed
▴ 120
0
votes
0
replies
151
views
pyscenic
pyscenic
scenic
2 days ago by
Andy
▴ 30
1
vote
1
reply
222
views
just one plot appears in the shiny application not all
plot
source
shiny
code
updated 2 days ago by
bkleiboeker
▴ 320 • written 2 days ago by
mrashad
▴ 60
0
votes
0
replies
152
views
Downsample process in ActiveRegion determination (HaplotypeCaller and Mutect2)
Downsample
Mutect2
HaplotypeCaller
2 days ago by
yxwucq
• 0
0
votes
0
replies
217
views
Simes method
simes
method
SNP
R
2 days ago by
Eliza
▴ 10
735 results • Page
1 of 15
Recent Votes
Answer: RNA-SEQ
Comment: RNA-SEQ
Comment: RNA-SEQ
Answer: RNA-SEQ
Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Popular Question
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Emy
▴ 40
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to
feiwu00
• 0
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to
paigemiller
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Scholar
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GenoMax
127k
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shpak.max
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hugo.avila
▴ 490
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TheCatalyst
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Recent Replies
Comment: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
![enter image description here][1] enter image description here ![enter image description here][2] [1]: /media/images/d06e761c-b715…
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Ruben
• 0
> Unfortunately, as far as I can tell, WDL provides no support for iterating over the contents of a directory. (I find this shocking. I con…
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial suppli…
Comment: RNA-SEQ
by
ali
• 0
thanks for your helping
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
by
iraun
5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
Andy
• 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39
by
seidel
11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard
by
ntsopoul
▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
thank you. i will go through it
Comment: Fastqc report analysis
by
npavliukovec
• 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number
by
kimgeng
• 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number
by
ntsopoul
▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript
by
ntsopoul
▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
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