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556 results • Page
1 of 12
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
54
views
Miseq mothur error with SOP in galaxy - Help please!
mothur
miseq
16s
Galaxy
sop
updated just now by
colindaven
4.4k • written 3 hours ago by
Melissa
• 0
0
votes
1
reply
39
views
Find corresponding branch from gene tree in species tree
phylogeny
family-tree
gene
species
phylogenetics
updated 40 minutes ago by
Ram
38k • written 2 hours ago by
Charlotte West
▴ 40
0
votes
2
replies
70
views
How can I creating multisample VCF file ?
VCF
updated 41 minutes ago by
Ram
38k • written 4 hours ago by
eennadi
▴ 20
0
votes
0
replies
54
views
How to identify the batch informations from the sample ID?
batch-correction
TCGAbatch
DESeq2
TCGA
updated 39 minutes ago by
Ram
38k • written 5 hours ago by
dare_devil
★ 1.7k
0
votes
1
reply
57
views
Adaptor sequences in GIAB samples
illumina
GIAB
adaptor
cutadapt
updated 4 hours ago by
GenoMax
125k • written 5 hours ago by
Mk
▴ 10
0
votes
3
replies
97
views
pileup consolidation tool
RNAseq
pileup
jacusa
samtools
6 hours ago by
joe
▴ 380
0
votes
2
replies
138
views
How I know the genome assembly quality by the low coverage Pacbio data ?
genome
Pacbio
6 hours ago by
wdpang
• 0
0
votes
0
replies
65
views
Stringtie prepDE.py script
deseq2
stringtie
updated 41 minutes ago by
Ram
38k • written 13 hours ago by
Aiswarya
• 0
0
votes
2
replies
101
views
Averaging across multiple proteomic experiments
statistics
proteomics
R
updated 1 hour ago by
ATpoint
68k • written 13 hours ago by
bhumm
▴ 20
0
votes
2
replies
126
views
Copy Number Variants, where to start?
CNV
annotation
31 minutes ago by
paolo
▴ 60
0
votes
0
replies
76
views
mosdepth coverage & transcripts per million
TPM
coverage
metagenome
mosdepth
16 hours ago by
hannahf
• 0
0
votes
2
replies
123
views
FATAL: While performing build: build image size <= 0 - Issues With Singularity
R
Docker
Singularity
1 hour ago by
Indira
• 0
0
votes
1
reply
102
views
Methods for downsampling coverage in a VCF
BCFTools
downsampling
WGS
sequencing
GATK
updated 16 hours ago by
Medhat
9.5k • written 16 hours ago by
a
• 0
0
votes
0
replies
79
views
Questions about HVGs and HEGs in single cell research
single-cell
machine-learning
updated 17 hours ago by
Ram
38k • written 18 hours ago by
me
• 0
0
votes
0
replies
73
views
average expression function and pct
seurat
average
pct
expression
and
19 hours ago by
rasing02
• 0
0
votes
0
replies
80
views
GoSemSIm - function mgeneSim() is resulting in similarity matrix without 1s od diagonal
vs
Gosim
GoSemSIm
20 hours ago by
eliska.ochodkova
• 0
0
votes
2
replies
148
views
Error with FindConservedMarkers()
FindConservedMarkers
20 hours ago by
Chris
▴ 60
0
votes
0
replies
88
views
Extract different variants of a vcf file comparing to other vcf files
gatk
bedtools
mutect2
vcftools
variant
3 hours ago by
minoo
▴ 10
0
votes
3
replies
191
views
BWA-mem not working with Snakemake + singularity
snakemake
bwa
singularity
updated 22 hours ago by
Jeremy Leipzig
21k • written 1 day ago by
brunobsouzaa
▴ 800
6
votes
4
replies
149
views
Equivalent to SeqMan alignment tool
SeqMan
alignments
1 day ago by
A_heath
▴ 120
0
votes
6
replies
223
views
Issue in import files in Metaboanalyst
file
import
vector
Metaboanalyst
atomic
1 day ago by
Andrea
▴ 10
0
votes
0
replies
99
views
database for better classification of illumina contigs
classification
illumina
contigs
NR
updated 1 day ago by
GenoMax
125k • written 1 day ago by
sapuizait
▴ 10
0
votes
3
replies
190
views
How to unzip a file with .bgz extention
.bgz
unzip
updated 1 day ago by
GenoMax
125k • written 1 day ago by
taniamahmood38
▴ 20
0
votes
0
replies
107
views
FWS calculation using plink data
vcf
Fws
Plink
1 day ago by
anithanagaraj93
• 0
0
votes
0
replies
112
views
qPCR missing data
Bioconductor
Analysis
Expression
qPCR
1 day ago by
Prerna
• 0
0
votes
0
replies
92
views
imputing haplotypes from variants in a VCF file - vcfIndexFile
practical
graph
haplotype
vcf
imputation
PHG
1 day ago by
matt.shenton
▴ 40
0
votes
0
replies
99
views
Pathway Analysis for Cancer Spatial Transcriptomics Characterization
Spatial
Pathway
Oncology
Transcriptomics
Enrichment
updated 1 day ago by
GenoMax
125k • written 1 day ago by
Flemming
• 0
1
vote
1
reply
137
views
difference between chip-seq and association study
association
chip-seq
TWAS
updated 1 day ago by
seidel
10k • written 1 day ago by
rheab1230
▴ 120
0
votes
1
reply
142
views
gff2bed fails with "Non-numeric start coordinate. "
bedops
updated 1 day ago by
Jimmy
• 0 • written 1 day ago by
scottbrainard
▴ 50
0
votes
0
replies
102
views
Using bigWigCompare to correct for input signal
chip
input
peaks
bigwig
deeptools
21 hours ago by
Maycon
• 0
0
votes
0
replies
98
views
Trying to understand the difference between between these two HGVS
hgvs
1 day ago by
curious
▴ 720
0
votes
0
replies
101
views
RagTag patch error--"tuple index out of range"
correction
ragtag
scaffolding
1 day ago by
schmiggle
• 0
0
votes
0
replies
104
views
network alignment and network regression
network
1 day ago by
Bogdan
★ 1.3k
0
votes
0
replies
97
views
Can't convert paired end BAM to bed using bedtools
BAM
BEDPE
updated 1 day ago by
GenoMax
125k • written 1 day ago by
oksana03fel
• 0
0
votes
0
replies
100
views
Why does bcftools call from different max-depth (-d) value in mpileup give inconstant GT values?
mpileup
pileup
vcf
calling
bcftools
variant
1 day ago by
magnolia
▴ 20
0
votes
1
reply
200
views
MetaboAnalyst: Interpreting Enrichment Analysis Results
enrichment
metabolomics
1 day ago by
eva_u
▴ 10
0
votes
4
replies
198
views
geom_errorbar not dodging or producing horizontal line
ggplot2
geom_errorbar
updated 1 day ago by
FrankStarling
▴ 30 • written 1 day ago by
bsp017
▴ 40
3
votes
5
replies
205
views
Size of two scRNA-Seq conditions
scRNA-Seq
1 day ago by
Chris
▴ 60
0
votes
0
replies
77
views
Mapping IDs to systematic names (GOSim, setevidencelevel() )
GOSim
1 day ago by
eliska.ochodkova
• 0
0
votes
1
reply
112
views
Novogene somatic results with GATK mutect2
Mutect2
Novogene
GATK
somatic
VCF
updated 2 days ago by
GenoMax
125k • written 2 days ago by
chrisgr
▴ 20
2
votes
5
replies
210
views
fastqc: Per base sequence content
illumina
metagenomic
fastqc
1 day ago by
khoojj
• 0
0
votes
0
replies
99
views
A question about Bioinformatik analysis and experimental design / comparing 2 experiments
DEseq2
Batch-effect
updated 2 days ago by
Ram
38k • written 2 days ago by
Frederik
• 0
0
votes
0
replies
106
views
Input data for LIMMA: unnormalised or vsn or other?
lima
normalisation
vns
2 days ago by
Sebastian Hesse
▴ 320
0
votes
0
replies
93
views
question of exonerate output
protein
gff
exonerate
annotation
2 days ago by
TN
• 0
0
votes
0
replies
111
views
Mis-paired primers
amplicon
primers
Mis-paired
2 days ago by
Sara
▴ 10
0
votes
0
replies
107
views
show amplicon like exon in UCSC/IGV
amplicon
2 days ago by
Sara
▴ 10
0
votes
2
replies
185
views
scATAC-seq workflow
Signac
scATAC-seq
2 days ago by
bioinformatics.girl
• 0
0
votes
0
replies
133
views
Set Y limits for ggplot with sec.axis
rstudio
ggplot
2 days ago by
JirMan
• 0
0
votes
1
reply
140
views
Filter InterProScan output for a specific function
interproscan
annotation
updated 2 days ago by
jv
▴ 800 • written 3 days ago by
Purger
• 0
0
votes
1
reply
162
views
f-index in treemix
treemix
introgression
f-index
3 days ago by
kk.mahsa
▴ 140
556 results • Page
1 of 12
Recent Votes
Comment: Bacterial metatranscriptomics with DESEQ2?
C: How to extend contigs from single-end reads?
C: How to extend contigs from single-end reads?
Answer: Seurat or Bioconductor for single cell RNA seq
Seurat or Bioconductor for single cell RNA seq
Answer: Seurat or Bioconductor for single cell RNA seq
Answer: Seurat or Bioconductor for single cell RNA seq
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Recent Awards •
All
Popular Question
to
mathavanbioinfo
▴ 70
Popular Question
to
cgds
▴ 10
Teacher
to
Basti
★ 1.3k
Teacher
to
shenwei356
7.8k
Scholar
to
GenoMax
125k
Supporter
to
bsp017
▴ 40
Popular Question
to
vrrani
▴ 10
Recent Replies
Comment: CNV Prediction Tools
by
Quentin M
▴ 60
Give a try to [CODEX2][1] [1]: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1578-y
Comment: Problem with tximport and plasmodium falciparum
by
bioinfo
▴ 20
Thank you. It does not seem to be that. I changed my script a bit. Now it looks like shown below: mart <- biomaRt::useMart("protists_…
Comment: Copy Number Variants, where to start?
by
paolo
▴ 60
I have found autoCNV, inCNV, and ClassifyCNV. The second one is for exomic CNVs only, and the third one does not run on Windows, but it mig…
Comment: BLAST reference genome indexing
by
GenoMax
125k
That is correct.
Comment: BLAST reference genome indexing
by
bhumm
▴ 20
Thanks for the explanation and links. So when calling the database in the for use, I call the prefix of all the 'subfiles' which invokes th…
Comment: Averaging across multiple proteomic experiments
by
bhumm
▴ 20
It is two biological replicates. I reasoned it as increasing N=2. For both biological replicates, it is ~13 controls vs ~13 disease conditi…
Comment: How to summarize the expression of a gene when having expression data from diffe
by
i.sudbery
16k
tximport will calculate the weighted effective transcript length, but it doesn't use that in its calculation of gene level expression. Both…
Comment: FATAL: While performing build: build image size <= 0 - Issues With Singularity
by
Indira
• 0
I was building a docker image I created on my computer on an HPC. It seems that due to some network issues I kept getting this FATAL messag…
Answer: Seurat or Bioconductor for single cell RNA seq
by
Lindsey
▴ 10
Seurat is an R package, so if you're used to work with other Bioconductor packages, you should be fine! Also the tutorials and manuals from…
Answer: Seurat or Bioconductor for single cell RNA seq
by
Basti
★ 1.3k
Bioconductor is a package repository so your question is not accurate. Maybe you hesitate between Seurat and other packages dedicated to sc…
Answer: fastq-dump split-spot and skip-technical
by
Larissa Graciano
• 0
The link to the blog post isn't working, I believe this is the updated one: https://edwards.flinders.edu.au/fastq-dump/
Comment: Find corresponding branch from gene tree in species tree
by
andres.firrincieli
3.1k
check Notung: [link][1] [1]: http://www.cs.cmu.edu/~durand/Notung/
Comment: Help please! Miseq SOP with galaxy toolsuite
by
Melissa
• 0
I have posted in their forum but I have not found a solution yet. I was posting here for an alternative help source. I am running mother…
Comment: How to summarize the expression of a gene when having expression data from diffe
by
dsull
★ 3.7k
tximport does something a bit more clever than simply summing up (it factors transcript length into consideration). If you're given TPMs, …
Comment: Help please! Miseq SOP with galaxy toolsuite
by
GenoMax
125k
It is unclear as to what your question is exactly about. Are you running `mothur` via Galaxy? If that is the case then please post this on …
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