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160 results • Page
3 of 4
Sort: Votes
Rank
Views
Votes
Replies
0
votes
1
reply
813
views
Filtering for homozygous reference alleles
SNP
sequence
genome
updated 6 days ago by
Ram
39k • written 3.8 years ago by
AGE
▴ 30
0
votes
1
reply
758
views
differential expression of geodataset using limma (input files)
R
gene
updated 1 day ago by
Ram
39k • written 3.4 years ago by
firstorthopedicdoctor
▴ 30
0
votes
0
replies
100
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
3 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
192
views
ATAC seq - Odd insert size distribution
atac
atac-seq
qc
updated 1 day ago by
Ram
39k • written 14 months ago by
emalekos
▴ 10
0
votes
1
reply
400
views
pal2nal -nogap -nomismatch options not working
pal2nal
updated 1 day ago by
Marie
• 0 • written 6 months ago by
pkfsantos
• 0
0
votes
1
reply
176
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 2 days ago by
ATpoint
73k • written 3 days ago by
akainth
▴ 10
0
votes
2
replies
780
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure
pymol
protein
pdb
python
41 minutes ago by
Aatif Hashmi
• 0
0
votes
1
reply
708
views
Is there bioinformatics tool to check cross hybridization between primers and probes?
primer
cross-hybridisation
pcr
updated 1 day ago by
Tawny
▴ 180 • written 2.7 years ago by
Pramod Shinde
• 0
0
votes
0
replies
10
views
cannot find genes with abricate and VFDB
abricate
wgs
vfdb
1 hour ago by
luciano.g
• 0
0
votes
0
replies
3
views
how to ensure that embedding for the new data is initialized based on the embedding of the existing data in UMAP?
UMAP
10 minutes ago by
Raheleh
▴ 250
0
votes
1
reply
155
views
Pairwise Alignment
Pairwise-Alignment
updated 3 days ago by
Ram
39k • written 4 days ago by
Fatemeh
• 0
0
votes
0
replies
137
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
5 days ago by
Manuel
• 0
0
votes
4
replies
655
views
Error in PGAP pangenome pipeline?
sequence
genome
sequencing
gene
updated 2 days ago by
Ram
39k • written 3.5 years ago by
Kumar
▴ 100
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
0
votes
0
replies
664
views
Resources recommendations for cloud computing (AWS) beginners
cloud
aws
hpc
updated 1 day ago by
Ram
39k • written 3.4 years ago by
m98
▴ 400
0
votes
2
replies
143
views
Blast reads classification
NGS
magicblast
blast
updated 20 hours ago by
Ram
39k • written 1 day ago by
Giulia.cosenza
▴ 80
0
votes
3
replies
155
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
6
replies
374
views
variant allelic fraction
vep
updated 2 days ago by
Ram
39k • written 4 days ago by
Jom
• 0
0
votes
1
reply
826
views
Error in MEGAHIT
Assembly
next-gen
metagenomic
updated 1 day ago by
Ram
39k • written 3.4 years ago by
nisrinalulu
▴ 10
0
votes
2
replies
1.0k
views
Find most upregulated genes in one library?
EdgeR
RNA-Seq
Rsubread
updated 3 days ago by
Ram
39k • written 3.7 years ago by
williams.damon26
▴ 10
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
0
replies
85
views
CIBERSORTx hires mode duplicates
CIBERSORT
CIBERSORTx
RNA-seq
bulk
deconvolution
1 day ago by
michaelhojungyoon
• 0
0
votes
0
replies
588
views
Proportion of traits in several groups
propotion-test
fishers-exact-test
updated 6 days ago by
Ram
39k • written 3.8 years ago by
biobiu
▴ 140
0
votes
0
replies
787
views
BWA MEM paramenter
alignment
sequencing
updated 1 day ago by
Ram
39k • written 3.3 years ago by
deniselavezzari
• 0
0
votes
0
replies
164
views
NMDS plotting issue
NMDS
metagenomic
6 days ago by
arshad1292
▴ 90
0
votes
2
replies
307
views
too many zeros in 16S rRNA amplicon sequencing data
16S
rRNA
2 days ago by
zhangdengwei
▴ 190
0
votes
1
reply
193
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 6 days ago by
raphael.B
▴ 360 • written 7 days ago by
sonsunjirachote
• 0
0
votes
0
replies
150
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
6 days ago by
OST
▴ 10
0
votes
1
reply
688
views
Small demo bioinformatics workflows which don't require reference data?
workflow
pipeline
updated 6 days ago by
Ram
39k • written 3.7 years ago by
steve
★ 3.3k
0
votes
5
replies
960
views
bigwigs to reads in peaks
R
atac-seq
updated 1 day ago by
Ram
39k • written 2.4 years ago by
pt.taklifi
▴ 60
0
votes
6
replies
1.9k
views
Variable read length distribution after cutadapt running for my ATAC-seq datasets
cutadapt
read-length
alignment
ATAC-seq
updated 1 day ago by
Ram
39k • written 3.1 years ago by
yaoyao20152031
• 0
0
votes
0
replies
1.1k
views
Assembly error on Ipyrad step 3: ERROR IPyradError(None)
rad-seq
ipyrad
updated 3 days ago by
Ram
39k • written 3.7 years ago by
mgpastos
▴ 10
0
votes
0
replies
269
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 1 day ago by
Ram
39k • written 9 weeks ago by
Chris
▴ 100
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
1
reply
388
views
How to quantification proteomics data
proteomics
updated 3 days ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
0
votes
0
replies
61
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
2 days ago by
Sapphire
• 0
0
votes
2
replies
228
views
How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?
differential-expression
TPM
GSEA
PANDA
16 hours ago by
John
• 0
0
votes
1
reply
105
views
GSEA application not launching
GSEA
updated 16 hours ago by
GenoMax
130k • written 16 hours ago by
Jen
▴ 40
0
votes
0
replies
162
views
busco id description
OrthoDB
BUSCO
updated 6 days ago by
Ram
39k • written 6 days ago by
angelina
• 0
0
votes
0
replies
86
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
1 day ago by
cate.cevallos
• 0
0
votes
8
replies
1.5k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 2 days ago by
Ram
39k • written 3.5 years ago by
muhammad.khizerkiet
• 0
0
votes
3
replies
842
views
meta-analysis of geo dataset
R
microarray
gene
updated 1 day ago by
Ram
39k • written 3.4 years ago by
firstorthopedicdoctor
▴ 30
0
votes
2
replies
774
views
Error in mvnX when running processSamples.R of OncoCNV
variant-calling
oncocnv
cnv
updated 2 days ago by
Ram
39k • written 3.5 years ago by
mwarrier
• 0
0
votes
0
replies
94
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 3 days ago by
Ram
39k • written 3 days ago by
beausoleilmo
▴ 530
0
votes
1
reply
262
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 6 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
0
votes
0
replies
296
views
Identifying Compotence Genes for Genetic Modification of strains
competence-genes
updated 1 day ago by
Ram
39k • written 3.2 years ago by
GTJR
• 0
0
votes
1
reply
137
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 1 day ago by
ATpoint
73k • written 1 day ago by
t.ru
▴ 20
0
votes
1
reply
117
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 1 day ago by
ATpoint
73k • written 1 day ago by
f2ff7a46
• 0
0
votes
2
replies
952
views
error while executing panX script (KeyError: 'db_xref').
linux
python
genome
biopython
updated 1 day ago by
Ram
39k • written 2.8 years ago by
Kumar
▴ 100
0
votes
1
reply
169
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 4 days ago by
Hamid Ghaedi
2.9k • written 5 days ago by
younglin113
▴ 50
160 results • Page
3 of 4
Recent Votes
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
Answer: Extract variants/SNPs with T>G substitution from a VCF file
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
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Recent Replies
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…
Comment: conda: command not found: gatk.
by
bestone
▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk.
by
bestone
▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
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