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122 results • Page
1 of 3
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0
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0
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1
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Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
just now by
firestar
★ 1.5k
0
votes
0
replies
8
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
11 minutes ago by
TJay
• 0
0
votes
0
replies
4
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
20 minutes ago by
predeus
★ 1.8k
0
votes
0
replies
22
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
48 minutes ago by
ucbtep
▴ 20
2
votes
5
replies
56
views
GATK GenotypeGVCFs explain
calling
gatk
variant
GenotypeGVCFs
updated 10 minutes ago by
Pierre Lindenbaum
153k • written 2 hours ago by
Sarah
▴ 30
1
vote
1
reply
159
views
TCGA Methylation Data and Gene Mapping
Methylation
Cancer
TCGA
updated 2 hours ago by
Basti
★ 1.4k • written 1 day ago by
James
▴ 30
1
vote
2
replies
154
views
How to implement this two-stage one-to-many workflow using WDL?
wdl
updated 3 hours ago by
Pierre Lindenbaum
153k • written 13 hours ago by
kynnjo
▴ 70
0
votes
0
replies
53
views
Dnaplotter
Artemis
3 hours ago by
prs
• 0
0
votes
2
replies
449
views
Databases to check variant pathogenicity
WholeExomeSequencing
updated 3 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 3 hours ago by
AtenaLia
▴ 20 • written 2.8 years ago by
Eugene A
▴ 170
1
vote
1
reply
88
views
How to create GO Bar Plot using data obtained from DAVID Functional Enrichment Analysis?
Plot
DAVID
R
updated 2 hours ago by
Basti
★ 1.4k • written 4 hours ago by
Stefanus C.B.
• 0
0
votes
1
reply
89
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 4 hours ago by
Mensur Dlakic
★ 23k • written 7 hours ago by
dgrace999
• 0
0
votes
0
replies
67
views
Obtain the GenomicRanges from segmented CNA data and the corresponding TSS for EnrichedPlot
TSS
GRanges
EnrichedPlot
promoters
GenomicRanges
9 hours ago by
melissachuaphd
• 0
0
votes
0
replies
68
views
ChIPseq w/ polyploid genome : Xenopus laevis
chipseq
alignment
xenopus
ploidy
12 hours ago by
William
▴ 10
0
votes
0
replies
98
views
Differential (pathways) expression testing using linear model packages in R (Limma & GSVA)
GSVA
limma
R
13 hours ago by
Tadeoye
▴ 30
1
vote
2
replies
126
views
How to adjust for multiple batches using Combat-Seq
ComBat
RNA-seq
updated 13 hours ago by
Ram
38k • written 13 hours ago by
sabriledesma13
• 0
0
votes
0
replies
87
views
How to quantify the expression of CD45 isoforms from bulk RNA-seq data
isoforms
Salmon
RNA-seq
CD45
13 hours ago by
eager_underdog
• 0
0
votes
4
replies
195
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
10 hours ago by
O.rka
▴ 650
0
votes
2
replies
148
views
Processing fastqs generated by inDrop protocol
single-cell
rna-seq
indrop
updated 12 hours ago by
Ram
38k • written 15 hours ago by
bobbybobbobbo
• 0
1
vote
3
replies
193
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 13 hours ago by
GenoMax
126k • written 16 hours ago by
Pegasus
▴ 80
0
votes
1
reply
99
views
Circos plot
circos
updated 2 hours ago by
Fabio Marroni
★ 3.0k • written 16 hours ago by
prs
• 0
0
votes
1
reply
95
views
mpileup2sync
mpileup2sync
population2
updated 15 hours ago by
Ram
38k • written 16 hours ago by
Hayler Edu
▴ 30
0
votes
1
reply
2.1k
views
Blog:
list of old gene name in C. elegans
c.elegans
gene
wormbase
updated 16 hours ago by
geneontologyhelp
▴ 190 • written 8.2 years ago by
firoz.imtech
▴ 50
3
votes
6
replies
271
views
Pig Reference Genome
Genome
updated 13 hours ago by
Joe
20k • written 16 hours ago by
anasjamshed
▴ 120
0
votes
0
replies
71
views
Number of gigabases necesary for Iso-seq-PacBio
Iso-seq
RNA-Seq
Alternative-Splicing
PacBio
updated 16 hours ago by
Ram
38k • written 17 hours ago by
Jesús M
• 0
0
votes
2
replies
368
views
how to create interacting Hi-C peaks
chromatin
interaction
gene
Hi-C
updated 18 hours ago by
Buffo
★ 2.0k • written 3 days ago by
rheab1230
▴ 140
0
votes
2
replies
135
views
GSVA scores - positive and negative values - normalization prior to running PCA
clr
normalization
GSVA
scale
17 hours ago by
Bianca
▴ 20
0
votes
2
replies
123
views
Problem with blasting UNMAPPED RNA-seq paired end reads in Jaculus jaculus
RNAseq
jaculus
unmapped
reads
17 hours ago by
barbarainb
• 0
0
votes
0
replies
57
views
PGx question regarding RSIDs with more than one variant associated with it
pharmacogenomics
rsid
pgx
18 hours ago by
Roy
▴ 10
0
votes
2
replies
150
views
How to calculate the Z value of infernal cmscan?
cmscan
ncRNA
infernal
updated 20 hours ago by
Dunois
★ 2.3k • written 21 hours ago by
shelvenlone
• 0
4
votes
5
replies
238
views
samtools idxstats not removing ChrM
samtools
ChIPseq
updated 13 hours ago by
benformatics
3.5k • written 22 hours ago by
Jen
▴ 40
1
vote
2
replies
129
views
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
pfam
protein
id
interpro
sequence
updated 21 hours ago by
GenoMax
126k • written 21 hours ago by
max
• 0
0
votes
0
replies
81
views
Converting Abricate output (.tsv) to gff3 format
gff3
convert
tsv
Abricate
21 hours ago by
ghataksnd
▴ 10
0
votes
0
replies
92
views
samtools mpileup - bases string explanation
samtools
mpileup
22 hours ago by
igorm
▴ 20
0
votes
3
replies
436
views
Practical Haplotype Graph -- Pathing Error
PHG
updated 23 hours ago by
lcj34
▴ 220 • written 25 days ago by
wcs98
• 0
0
votes
3
replies
203
views
Problem in converting SAM to BAM file by DROP SEQ
SAMtoBAM
updated 15 hours ago by
Ram
38k • written 1 day ago by
VANSHIKA
• 0
6
votes
5
replies
311
views
Trying to install Roary with Conda results in error message
roary
conda
2 hours ago by
tobiwan
▴ 10
1
vote
1
reply
229
views
What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k_v1 in biomart?
genetics
biomaRt
gene
updated 13 hours ago by
Ram
38k • written 2 days ago by
solarchan7
• 0
0
votes
1
reply
176
views
Error while running Virusfinder
Virusfinder
updated 16 hours ago by
Ram
38k • written 1 day ago by
DC
• 0
6
votes
5
replies
358
views
Where do find virulence gene information in a gff/gtf file?
microbial
genomics
gff
annotation
gtf
updated 19 hours ago by
oschwengers
▴ 100 • written 1 day ago by
sovrappensiero
▴ 60
1
vote
3
replies
238
views
FeatureCounts >edgeR > GO
RNA-SEQ
updated 2 hours ago by
Basti
★ 1.4k • written 1 day ago by
Pegasus
▴ 80
2
votes
6
replies
582
views
Bad quality fastq files for analysis
quality
bad
DNA-seq
fastq
alignment
3 hours ago by
Gene_MMP8
▴ 220
3
votes
2
replies
299
views
Human Population Reference Genomes (+Neanderthal?)
comparative-genomics
updated 16 hours ago by
Ram
38k • written 2 days ago by
emm008
• 0
0
votes
1
reply
209
views
Circos plot using vcf : Mutect2 MultiSample VCF out file
Mutect2
vcf
updated 15 hours ago by
Ram
38k • written 2 days ago by
m. bioinfo
• 0
2
votes
2
replies
248
views
Nextflow Stringtie: command not found Error
nextflow
rna-seq
stringtie
updated 22 hours ago by
ATpoint
70k • written 2 days ago by
selenaajohn
• 0
4
votes
7
replies
544
views
How to perform synteny alignments and plots only with a gene?
Comparative
Evolution
Alignment
Synteny
Genomics
updated 12 hours ago by
cmdcolin
★ 2.9k • written 3 days ago by
Rafael Soler
★ 1.1k
0
votes
2
replies
290
views
Post-Imputation QC Problem
Imputation
17 hours ago by
Jesse
• 0
6
votes
11
replies
647
views
Calculate RPKM
RPKM
5 hours ago by
Chris
▴ 70
3
votes
6
replies
515
views
Chromosome "whole genome shotgun sequence" not found
samtools
mpileup
16 hours ago by
Hayler Edu
▴ 30
3
votes
3
replies
367
views
Downloading required resources for VQSR
VQSR
WGS
sequencing
genome
WES
updated 15 hours ago by
Ram
38k • written 5 weeks ago by
Yoosef
▴ 50
122 results • Page
1 of 3
Recent Votes
Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?
Is There A Way To Run Fastqc On All The Fastq Files In The Different Directories With Just One Command?
Comment: samtools idxstats not removing ChrM
The Biostar Handbook. A bioinformatics e-book for beginners.
Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
Converting mapped + unmapped BAM files to raw FASTQ (RNA-seq data)
Comment: GATK GenotypeGVCFs explain
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TJay
• 0
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predeus
★ 1.8k
Popular Question
to
eennadi
▴ 20
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shenwei356
7.9k
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Zhilong Jia
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Recent Replies
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
thank you
Comment: GATK GenotypeGVCFs explain
by
raphael.B
▴ 270
It limits the operation to some genomic regions given as parameter
Comment: GATK GenotypeGVCFs explain
by
Sarah
▴ 30
what does the option L
Comment: GATK GenotypeGVCFs explain
by
Pierre Lindenbaum
153k
GenotypeGVCFs takes a set of GVCF files called with HaplotyperCaler and output a VCF file.
Answer: TCGA Methylation Data and Gene Mapping
by
Basti
★ 1.4k
CpGs may be annotated to more than >1 gene simply because gene regions overlap on the genome. If you want to associate each gene to a me…
Comment: Circos plot
by
Fabio Marroni
★ 3.0k
Please give a look to [this post][1] for increasing the probability to get an answer. If I may add some needed info: 1. What exactly do y…
Comment: Trying to install Roary with Conda results in error message
by
tobiwan
▴ 10
Wow, thank you so much for your explanation! My conda channel is indeed set to strict priority. Should packages with different dependencie…
Comment: FeatureCounts >edgeR > GO
by
Basti
★ 1.4k
You can use BioMart to convert your "gene-IDs" to gene symbols, but you need to specify from which database your gene identifiers come from
Comment: How to create GO Bar Plot using data obtained from DAVID Functional Enrichment A
by
Basti
★ 1.4k
If you search "DAVID dotplot" on this forum, you have many answers to your question. Note that you can also perform DAVID Functional Enrich…
Answer: How to implement this two-stage one-to-many workflow using WDL?
by
Pierre Lindenbaum
153k
nottested, something like: ``` version 1.0 workflow BIOSTAR { call FIRST { } scatter (F in FIRST.each_F)…
Answer: Databases to check variant pathogenicity
by
AtenaLia
▴ 20
You can try https://genebe.net , it is similar to Varsome though...
Answer: ACMG assignment tools
by
AtenaLia
▴ 20
Hi, free ACMG implementation without restrictions can be found at https://genebe.net . AFAIK there is also a free API coming.
Comment: Bad quality fastq files for analysis
by
Gene_MMP8
▴ 220
I don't have the data available. I want to identify such datasets. The overall aim is to determine what factors influence fastq data qualit…
Comment: mrbayes segmentation fault
by
Mensur Dlakic
★ 23k
I don't know what exactly the error message means. What I can tell you is that a burn-in of 2500 generations is absolutely inadequate. That…
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