Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
608 results • Page
1 of 13
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
16
views
multiqc: group samples by population + boxplot ?
multiqc
23 minutes ago by
Pierre Lindenbaum
155k
0
votes
0
replies
8
views
how to ensure that embedding for the new data is initialized based on the embedding of the existing data in UMAP?
UMAP
1 hour ago by
Raheleh
▴ 250
0
votes
0
replies
14
views
cannot find genes with abricate and VFDB
abricate
wgs
vfdb
2 hours ago by
luciano.g
• 0
1
vote
1
reply
569
views
target vs. bait BED files for Illumina WES
sequencing
Illumina
WES
whole-exome
updated 3 hours ago by
Sounkou-bioinfo
• 0 • written 10 months ago by
Juan Cordero
▴ 120
1
vote
1
reply
59
views
Filtering content in heatmap to highest values
R
heamap
ggplot
updated 3 hours ago by
Papyrus
★ 2.5k • written 4 hours ago by
cthangav
▴ 50
2
votes
1
reply
66
views
A question about the raw RNA-seq processing workflow
GDC
RNA-seq
STAR
Ubuntu
updated 4 hours ago by
Dr William Klubinski
▴ 110 • written 4 hours ago by
wyt1995
▴ 10
4
votes
7
replies
153
views
conda: command not found: gatk.
conda
gatk
updated 58 minutes ago by
GenoMax
130k • written 5 hours ago by
bestone
▴ 20
1
vote
2
replies
232
views
If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates?
read
groups
bam
addorreplacereadgroups
13 hours ago by
javiflaja
• 0
0
votes
0
replies
74
views
Changing gap open and extension penalties in muscle (or any other command line tool that works on mac, really)
multiple
sequence
alignment
16 hours ago by
sodiumnitrate
▴ 20
0
votes
0
replies
85
views
How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific
strandness
RNAseq
17 hours ago by
Sib
▴ 40
0
votes
1
reply
106
views
GSEA application not launching
GSEA
updated 17 hours ago by
GenoMax
130k • written 17 hours ago by
Jen
▴ 40
0
votes
0
replies
71
views
Using Tumor Immune Dysfunction and Exclusion (TIDE)
TPM
cancer
r
updated 21 hours ago by
Ram
39k • written 22 hours ago by
JACKY
▴ 100
0
votes
0
replies
72
views
question related to novel mirna file from miRDeep2?
miRDeep2
22 hours ago by
kuttibiotech2009
▴ 30
0
votes
0
replies
88
views
How to create a haplotype map?
picard
haplotype
CrosscheckFingerprints
updated 21 hours ago by
Ram
39k • written 1 day ago by
jgarces
▴ 30
0
votes
2
replies
144
views
Blast reads classification
NGS
magicblast
blast
updated 21 hours ago by
Ram
39k • written 1 day ago by
Giulia.cosenza
▴ 80
4
votes
4
replies
210
views
Normalized counts bulk RNA-seq to DEGs
RNA-seq
updated 23 hours ago by
ATpoint
73k • written 1 day ago by
t.ru
▴ 20
0
votes
0
replies
61
views
Required input files for COHCAP
TCGA
Methylation
input
COHCAP
1 day ago by
dilrajkaur766
• 0
0
votes
2
replies
119
views
Chain file for Homo_sapiens_assembly38.fasta to liftover Nebula vcf
hg38
fasta
hg19
chainfile
1 day ago by
berndmann
▴ 10
0
votes
1
reply
121
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly
removal
bacterial
genome
vector
updated 1 day ago by
GenoMax
130k • written 1 day ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
229
views
How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?
differential-expression
TPM
GSEA
PANDA
17 hours ago by
John
• 0
1
vote
1
reply
114
views
Plotting GO enrichment DATA
R
GO
enrichment-analysis
updated 22 hours ago by
Ram
39k • written 1 day ago by
hellokwmin
• 0
0
votes
0
replies
81
views
Popcorn using SNPs with extremely low P-value
Popcorn
SNP
1 day ago by
Apprentice
▴ 160
1
vote
1
reply
150
views
UCSC genome browser
Genome-browser
shannon-entropy
updated 22 hours ago by
Ram
39k • written 1 day ago by
Lkhagvadulam
• 0
0
votes
0
replies
86
views
CIBERSORTx hires mode duplicates
CIBERSORT
CIBERSORTx
RNA-seq
bulk
deconvolution
1 day ago by
michaelhojungyoon
• 0
0
votes
0
replies
102
views
Copy Number Alteration and Loss or Heterozygosity
LOH
CNA
copy-number
updated 22 hours ago by
Ram
39k • written 1 day ago by
Bogdan
★ 1.3k
0
votes
1
reply
138
views
How to add annotation columns with specific colors to the heatmap?
R
heatmap
RNA-seq
updated 22 hours ago by
Ram
39k • written 1 day ago by
ahmad mousavi
▴ 750
0
votes
3
replies
156
views
CellRanger problem
RNA-seq
STAR
scRNA
updated 1 day ago by
Arup Ghosh
3.2k • written 1 day ago by
Carlos Eduardo
• 0
0
votes
5
replies
211
views
VCF file CSQ flag
vcf
exome-sequencing
updated 1 day ago by
Ram
39k • written 1 day ago by
Payal
▴ 140
0
votes
0
replies
94
views
normalize for sample size in single cell rna seq cluster frequencies data
scRNAseq
seurat
10x
1 day ago by
chi.delta
▴ 40
1
vote
1
reply
129
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 1 day ago by
GenoMax
130k • written 1 day ago by
saint-even
• 0
0
votes
0
replies
87
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
1 day ago by
dilrajkaur766
• 0
0
votes
0
replies
92
views
m6A-seq input normalisation with RNA-seq
m6A-seq
MeRIP-Seq
normalisation
deepTools
updated 1 day ago by
Ram
39k • written 1 day ago by
Parichitran
• 0
0
votes
1
reply
151
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 1 day ago by
Ram
39k • written 1 day ago by
aaronlogsdon2001
• 0
0
votes
0
replies
86
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
2 days ago by
cate.cevallos
• 0
1
vote
4
replies
228
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 1 day ago by
ATpoint
73k • written 2 days ago by
Zhichao
• 0
0
votes
1
reply
117
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 2 days ago by
ATpoint
73k • written 2 days ago by
f2ff7a46
• 0
0
votes
1
reply
137
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 2 days ago by
ATpoint
73k • written 2 days ago by
t.ru
▴ 20
0
votes
2
replies
148
views
Visualizing several genomes/plasmids in a single figure
visualization
1 day ago by
blur
▴ 270
1
vote
1
reply
130
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 1 day ago by
GenoMax
130k • written 2 days ago by
lait
▴ 170
0
votes
0
replies
61
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
2 days ago by
Sapphire
• 0
0
votes
0
replies
85
views
Complex Phylogenetic Tree Annotation
annotation
protein
phylogenetic-tree
updated 1 day ago by
Ram
39k • written 2 days ago by
Aanushka
• 0
0
votes
2
replies
1.7k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 2 days ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
1
vote
3
replies
171
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 2 days ago by
Darked89
4.4k • written 2 days ago by
Ayish
• 0
0
votes
1
reply
115
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 2 days ago by
seidel
11k • written 2 days ago by
dare_devil
★ 3.1k
0
votes
2
replies
188
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
2 days ago by
JACKY
▴ 100
0
votes
1
reply
132
views
CIBERSORT Error: File not found
CIBERSORT
updated 2 days ago by
ATpoint
73k • written 2 days ago by
jcara514
• 0
3
votes
4
replies
259
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 1 day ago by
Ram
39k • written 2 days ago by
shamza
• 0
0
votes
3
replies
267
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 2 days ago by
Ram
39k • written 2 days ago by
Researcher
• 0
1
vote
0
replies
128
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
2 days ago by
zhangdengwei
▴ 190
1
vote
2
replies
211
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
1 day ago by
tahsinkhan570
• 0
608 results • Page
1 of 13
Recent Votes
Comment: Normalized counts bulk RNA-seq to DEGs
Comment: Normalized counts bulk RNA-seq to DEGs
Comment: Normalized counts bulk RNA-seq to DEGs
Tools To Calculate Average Coverage For A Bam File?
Comment: conda: command not found: gatk.
Answer: Finding Enhancers using Genomation library
Comment: If I execute "AddOrReplaceReadGroups" on a sarted and duplicate-marked .bam fil
Recent Locations •
All
France/Nantes/Institut du Thorax - INSERM UMR1087,
3 minutes ago
United States,
4 minutes ago
Ireland,
5 minutes ago
São Paulo - Brazil - Unifesp,
8 minutes ago
France,
9 minutes ago
Bologna,
11 minutes ago
Italy,
12 minutes ago
Recent Awards •
All
Commentator
to
Sasha
▴ 420
Teacher
to
e.r.zakiev
▴ 70
Popular Question
to
Raheleh
▴ 250
Popular Question
to
nishimalhotra2612
▴ 50
Popular Question
to
Omics data mining
▴ 220
Supporter
to
666billgaytes
▴ 10
Teacher
to
Alexander
▴ 110
Recent Replies
Answer: DevelopMed MSCA COFUND Fellowship Programme in Precision Oncology
by
developmed
• 0
Deadline extended to June 25, 2023 (23:59 GMT).
Answer: Is NA12878 Illumina Platinum set wgs or wes dataset
by
GenoMax
130k
Platinum 12878 is a whole genome sequence dataset. --> https://www.illumina.com/platinumgenomes.html
Comment: conda: command not found: gatk.
by
GenoMax
130k
Follow directions provided by `GATK` project: https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-…
Answer: What's the correct way to store bam record in a vector and free them?
by
Pierre Lindenbaum
155k
You should allocate a new pointer for each SAM record. I would do something like this (not tested): ``` std::vector<bam1_t*> record_list…
Comment: Creating a local version of Clustered NR database
by
GenoMax
130k
Thanks for those stats. So using clustered `nr` will still require significant hardware. Though this will save time as well.
Comment: Can I send my PyMol results to a web-page as a result for a submitted query? If
by
Aatif Hashmi
• 0
Basically I only want to show bases with disulphide bonds. like imagine I have a disulphide bond at 68 cys residue along with 145 cys. I …
Answer: How do I specify the Recalibration_data.table for "PrintReads" in GATK 4.3, if t
by
Pierre Lindenbaum
155k
do you want ApplyBQSR "Apply base quality score recalibration " ? https://gatk.broadinstitute.org/hc/en-us/articles/360036856671-ApplyBQSR
Comment: target vs. bait BED files for Illumina WES
by
Sounkou-bioinfo
• 0
Hi @jacorvar , did you find the answer to that question ?
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
That's an excellent point. A significant number of students are engaged in academic misconduct due to the use of fabricated references and …
Comment: Filtering content in heatmap to highest values
by
Papyrus
★ 2.5k
You mean something like this? depends on how you define "top" row or column # Create example (it is a data.table) ListerTFHeat <- …
Comment: conda: command not found: gatk.
by
666billgaytes
▴ 10
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file
by
4galaxy77
2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Traffic: 1919 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6