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108,940 results • Page
1 of 2179
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Does it possible to know what are the adjacent genes up to 1000bp upstream and downstream of IS element
Transposons
just now by
Neel
▴ 10
0
votes
1
reply
588
views
activity of unloaded/unassembled Tn5
sequencing
next-gen
updated 20 minutes ago by
callumjcparr
• 0 • written 5.1 years ago by
zhaohainancau
• 0
3
votes
2
replies
97
views
Problem generating a .vcf after upgrade of samtools and bcftools
vcf
bam
samtools
bcftools
2 hours ago by
Andy
• 0
0
votes
0
replies
34
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
4 hours ago by
rheab1230
▴ 140
0
votes
2
replies
84
views
My fastq files(paired end) have different read number
fastq
mapping
5 hours ago by
kimgeng
• 0
0
votes
2
replies
116
views
Can I use abundance from Tximport to compare the expression level of transcript in same condition?
Salmon
Tximport
updated 5 hours ago by
ntsopoul
▴ 20 • written 10 hours ago by
aimanbarki
▴ 20
1
vote
4
replies
148
views
Fastqc report analysis
fastqc
Fastqc
report
help
trim_galore
4 hours ago by
npavliukovec
• 0
727
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 7 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
96k
0
votes
1
reply
70
views
Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq data
splicing
RNA-seq
updated 2 hours ago by
iraun
5.8k • written 6 hours ago by
ntsopoul
▴ 20
0
votes
2
replies
103
views
Creating loop for read groups using Picard
bash
picard
loop
updated 3 hours ago by
ntsopoul
▴ 20 • written 7 hours ago by
brandnewatthis
• 0
0
votes
1
reply
77
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
2
votes
4
replies
2.6k
views
Need help teasing out insertions and deletions with bcftools stats file.vcf > file.stats
bcftools
indel
vcf
insertion
deletion
updated 8 hours ago by
Afif Elghraoui
• 0 • written 5.0 years ago by
oars
▴ 190
0
votes
2
replies
130
views
known-sites for Felis_catus_9.0 (GCA_000181335.4)
Felis-catus
GATK
9 hours ago by
makarov
• 0
1
vote
0
replies
78
views
Creating sample groups from a combination of genes for survival analysis
Survival
8 hours ago by
krushnach80
★ 1.1k
4
votes
5
replies
195
views
RNA-SEQ
NGS
RNA-SEQ
48 minutes ago by
ali
• 0
1
vote
4
replies
176
views
Creating a loop to mark duplicates using Picard
bash
picard
updated 9 hours ago by
Ram
38k • written 12 hours ago by
brandnewatthis
• 0
2
votes
3
replies
117
views
Active enhancers for mm39
bed
coordinates
enhancers
mm39
updated 3 hours ago by
seidel
11k • written 12 hours ago by
Marco Pannone
▴ 690
0
votes
0
replies
61
views
News:
course - Reproducibility in Bioinformatics
Bioinformatics
Docker
Reproducibility
12 hours ago by
carlopecoraro2
★ 2.3k
0
votes
4
replies
155
views
Mapping paired end reads with ngm and samtools, using prefixes and suffixes for creating vcf eventually
ngm
sam
samtools
updated 11 hours ago by
Ram
38k • written 12 hours ago by
Human
• 0
3
votes
2
replies
122
views
Power analysis for patient samples
RNA-seq
11 hours ago by
aropri
▴ 130
0
votes
3
replies
291
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2
vcf
updated 13 hours ago by
Pierre Lindenbaum
153k • written 2 days ago by
m. bioinfo
• 0
0
votes
0
replies
67
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
13 hours ago by
HERMAN
▴ 10
4
votes
2
replies
132
views
Forum:
advice on course selection for a bioinformatics career.
career
updated 13 hours ago by
Istvan Albert
96k • written 14 hours ago by
Aaron
• 0
0
votes
0
replies
54
views
Error when using compareCluster from enichment
compareCluster
13 hours ago by
jacob
• 0
0
votes
0
replies
71
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
95
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 13 hours ago by
GenoMax
127k • written 14 hours ago by
emmanouil.a
▴ 110
0
votes
2
replies
122
views
How to add gene information below the BSmooth result ?
BSmooth
methylation
DNA
8 hours ago by
diqixiaoyaoer
▴ 10
1
vote
1
reply
111
views
Plot in R: Presence of bacteria type A vs bacteria type B in different groups
boxplot
phyloseq
plot
abundance
ggplot2
R
updated 14 hours ago by
Basti
★ 1.4k • written 15 hours ago by
flourde
• 0
2
votes
1
reply
82
views
Fastqc lsequence duplication and per base sequence content failed
RNA-seq
fastqc
updated 15 hours ago by
GenoMax
127k • written 15 hours ago by
waqaskhokhar999
▴ 150
3
votes
11
replies
453
views
prefix extraction and preparation for mapping and variant calling
bash
updated 15 hours ago by
GenoMax
127k • written 4 days ago by
Human
• 0
3
votes
4
replies
1.3k
views
Nextflow memory issues custom config -c
nextflow
updated 14 hours ago by
ATpoint
70k • written 14 months ago by
louisber2765
• 0
2
votes
3
replies
148
views
wrong quality plots in fastqc output
fastqc
quality
samtools
fastq
wgsim
11 hours ago by
poecile.pal
▴ 50
1
vote
5
replies
264
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 18 hours ago by
TJay
• 0
6
votes
8
replies
314
views
6 follow
Snakemake vs Nextflow Upcoming bioinformatics Project
Programming
Masters
8 hours ago by
rackbersingh
• 0
0
votes
1
reply
101
views
Why GATK is slow with haplotypecalling
GATK
HaplotypeCalling
updated 16 hours ago by
Pierre Lindenbaum
153k • written 17 hours ago by
rj.rezwan
• 0
0
votes
0
replies
79
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
17 hours ago by
zhangfish
▴ 40
0
votes
0
replies
67
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
17 hours ago by
Joana
• 0
0
votes
0
replies
104
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
18 hours ago by
firestar
★ 1.5k
0
votes
0
replies
87
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
18 hours ago by
predeus
★ 1.8k
0
votes
0
replies
89
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
202
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 18 hours ago by
Pierre Lindenbaum
153k • written 20 hours ago by
Sarah
▴ 30
3
votes
1
reply
234
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
updated 20 hours ago by
Basti
★ 1.4k • written 2 days ago by
James
▴ 30
4
votes
2
replies
251
views
How to implement this two-stage one-to-many workflow using WDL?
wdl
updated 21 hours ago by
Pierre Lindenbaum
153k • written 1 day ago by
kynnjo
▴ 70
0
votes
0
replies
116
views
Dnaplotter
Artemis
21 hours ago by
prs
• 0
0
votes
2
replies
506
views
Databases to check variant pathogenicity
WholeExomeSequencing
updated 22 hours ago by
AtenaLia
▴ 20 • written 13 months ago by
Fatemeh Nabizadeh
▴ 10
11
votes
13
replies
4.1k
views
8 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 22 hours ago by
AtenaLia
▴ 20 • written 2.8 years ago by
Eugene A
▴ 170
1
vote
1
reply
160
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
150
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 23 hours ago by
Mensur Dlakic
★ 23k • written 1 day ago by
dgrace999
• 0
0
votes
0
replies
116
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
108
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
1 day ago by
William
▴ 10
108,940 results • Page
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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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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 supp…
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…
Comment: Easy way to split VCF file by chromosome
by
Joana
• 0
You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis
by
ntsopoul
▴ 20
I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
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