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88 results • Page
1 of 2
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Votes
Replies
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
78
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
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
1
reply
161
views
Circos plot
circos
updated 21 hours ago by
Fabio Marroni
★ 3.0k • written 1 day ago by
prs
• 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
2
votes
5
replies
520
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 9 hours ago by
igor
13k • written 4 days ago by
e.r.zakiev
▴ 30
1
vote
4
replies
344
views
Loading Traitdata file for WGCNA analysis
R
WGCNA
updated 13 hours ago by
Ram
38k • written 5 months ago by
priya.bmg
▴ 50
0
votes
0
replies
375
views
Using infercnv R package
r
infercnv
Seurat
annotation
updated 13 hours ago by
Ram
38k • written 6 months ago by
j.jacob1
• 0
0
votes
16
replies
1.4k
views
How to convert ncbi gff file to ensembl gff format
bcftools
gff
updated 11 hours ago by
Ram
38k • written 6 months ago by
yoser4
▴ 10
0
votes
2
replies
328
views
Can't create index file of Bam file
bam
samtools
updated 11 hours ago by
Ram
38k • written 7 months ago by
Zahed Alam
• 0
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 11 hours ago by
Ram
38k • written 7 months ago by
Jacob
• 0
0
votes
1
reply
280
views
Batch rename fasta file of RefSeq
fasta
refseq
updated 11 hours ago by
Ram
38k • written 7 months ago by
BATMAN
• 0
0
votes
0
replies
188
views
PSL file confusion on negative strand
BLAT
PSL
updated 11 hours ago by
Ram
38k • written 8 months ago by
spark
• 0
0
votes
0
replies
187
views
Comparing PopoolationTE2 output with reference .bed file in Python
bed
python
pandas
PopoolationTE2
updated 11 hours ago by
Ram
38k • written 8 months ago by
Emilia
• 0
0
votes
2
replies
374
views
Which database should I get variant data from WGS for Asian and AA populations
vcf
WGS
variant
database
updated 11 hours ago by
Ram
38k • written 8 months ago by
minghuiguo448
• 0
0
votes
0
replies
275
views
SURVIVOR bed file
BED
CNV
SURVIVOR
VCF
updated 11 hours ago by
Ram
38k • written 8 months ago by
Nameless
• 0
0
votes
3
replies
397
views
splitting a bam file by XA tag into multiple lines
bam
BWA
updated 11 hours ago by
Ram
38k • written 9 months ago by
eric.londin
▴ 50
0
votes
3
replies
369
views
Annovar file to maf file conversion
maf
R
annovar
updated 11 hours ago by
Ram
38k • written 9 months ago by
ganeshram
• 0
0
votes
0
replies
170
views
Save Scene File in PDB in YASARA
YASARA
SCENE
PDB
updated 11 hours ago by
Ram
38k • written 9 months ago by
misbahnaseem95
• 0
0
votes
0
replies
187
views
How to convert .bed/.bim/.fam file to .dat file to run --dosage command to get INFO
plink
dosage
updated 11 hours ago by
Ram
38k • written 9 months ago by
Raju
• 0
1
vote
1
reply
376
views
LFTP fails to submit files to the EGA sequence database
lftp
EGA
updated 10 hours ago by
Ram
38k • written 10 months ago by
heskett
▴ 100
0
votes
2
replies
399
views
How to remove evidence tags and unnecessary information in the uniprot tab file
UNIPROT
updated 10 hours ago by
Ram
38k • written 10 months ago by
devhimd
▴ 10
0
votes
3
replies
425
views
GC @5,20,50 : Fraction of GC content in the bases around the variant position
fasta
genome
GC-content
updated 10 hours ago by
Ram
38k • written 10 months ago by
Maryem
▴ 10
0
votes
1
reply
329
views
I have two different libaries which were sequenced, How should I compare their library diversity?
bam
sam
updated 15 hours ago by
Ram
38k • written 10 months ago by
zt10122
▴ 20
0
votes
0
replies
156
views
How to generate a bed file indicating increased ratio of H3K4me3 to H3K4me1
H3K4me3
bed
H3K4me1
updated 10 hours ago by
Ram
38k • written 10 months ago by
jia
• 0
0
votes
0
replies
163
views
MEME motif discovery
fasta
updated 10 hours ago by
Ram
38k • written 10 months ago by
kaisakaiho73847
• 0
1
vote
1
reply
453
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 10 hours ago by
Ram
38k • written 10 months ago by
ManuelDB
▴ 30
0
votes
5
replies
485
views
BAM file became smaller after merging
BAM
updated 10 hours ago by
Ram
38k • written 10 months ago by
kimmitzka
• 0
0
votes
0
replies
225
views
Tapestry scDNA-seq and translocations
scDNA-seq
H5
single-cell
MOSAIC
variant-calling
updated 9 hours ago by
Ram
38k • written 11 months ago by
jmnz22
• 0
88 results • Page
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Answer: RNA-SEQ
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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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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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