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156 results • Page
3 of 4
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644
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News:
CFP Special Collection: Parallel Computing in Evolutionary Bioinformatics, SAGE Journal, JCR 2.203 (Q2)
CFP
updated 17 hours ago by
Ram
39k • written 3.8 years ago by
jlguisado
• 0
0
votes
0
replies
635
views
News:
Training in Creating Plots, Graphs and Maps using R @ NIH
Biomedical
next-gen
Data-analysis
updated 15 hours ago by
Ram
39k • written 3.8 years ago by
AABI
▴ 130
0
votes
0
replies
634
views
News:
EMBO | EMBL Symposium: The Four-Dimensional Genome
microscopy
genome
DNA
genomics
updated 15 hours ago by
Ram
39k • written 3.8 years ago by
EMBL Events
• 0
0
votes
0
replies
610
views
News:
Statistics using R
R
updated 14 hours ago by
Ram
39k • written 3.7 years ago by
carlopecoraro2
★ 2.3k
0
votes
0
replies
595
views
News:
Coding In The Cloud For Biomedical Researchers - Hands-On Training - Live Cast
next-gen-sequencing
rna-seq
ChIP-Seq
updated 16 hours ago by
Ram
39k • written 3.8 years ago by
AABI
▴ 130
3
votes
0
replies
591
views
News:
Testing and feedback of upcoming salmon release
salmon
RNA-Seq
updated 14 hours ago by
Ram
39k • written 3.7 years ago by
Rob
6.1k
1
vote
0
replies
589
views
News:
Cellosaurus release 32 is available
knowledgebase
database
cell-line
updated 14 hours ago by
Ram
39k • written 3.7 years ago by
Amos Bairoch
▴ 110
0
votes
0
replies
586
views
Proportion of traits in several groups
propotion-test
fishers-exact-test
updated 16 hours ago by
Ram
39k • written 3.8 years ago by
biobiu
▴ 140
0
votes
0
replies
565
views
News:
Comparative Genomics Workshop . registration deadline
assembly
Pacbio
updated 15 hours ago by
Ram
39k • written 3.8 years ago by
carlopecoraro2
★ 2.3k
1
vote
0
replies
547
views
Job:
Statistician/Bioinformatician at the ICR, Sutton, UK
ngs
updated 15 hours ago by
Ram
39k • written 3.8 years ago by
zx8754
11k
0
votes
0
replies
534
views
Online courses/studies bioinformatics
online-study
learning
updated 16 hours ago by
Ram
39k • written 3.8 years ago by
MAR
• 0
2
votes
0
replies
509
views
News:
Introduction to RMarkdown
R
updated 15 hours ago by
Ram
39k • written 3.8 years ago by
carlopecoraro2
★ 2.3k
0
votes
0
replies
478
views
News:
Comparative Genomics course in October - last 2 places left
Illumina
Pacbio
nanopore
next-gen
updated 13 hours ago by
Ram
39k • written 3.7 years ago by
carlopecoraro2
★ 2.3k
2
votes
1
reply
477
views
How to enter bioinformatics programme
career
updated 16 hours ago by
Ram
39k • written 3.8 years ago by
wierdrequests
• 0
0
votes
1
reply
340
views
Diffbind not calling sites as differentially bound
DiffBind
updated 22 hours ago by
Rory Stark
★ 1.7k • written 9 months ago by
ipsc-jl
• 0
3
votes
3
replies
321
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling
VEP
COSMIC
19 hours ago by
bt_cepo
▴ 20
0
votes
8
replies
291
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 23 hours ago by
GenoMax
129k • written 2 days ago by
Marta
• 0
2
votes
7
replies
286
views
What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein
alignment
updated 5 hours ago by
Vincent Laufer
★ 2.9k • written 21 hours ago by
Alexander
▴ 70
0
votes
5
replies
285
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
updated 20 hours ago by
lcj34
▴ 230 • written 3 days ago by
jrodrigu
• 0
1
vote
7
replies
283
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP
GATK
updated 18 hours ago by
Ram
39k • written 1 day ago by
mohsamir2016
▴ 30
2
votes
7
replies
260
views
How to sort gff3 according to chromosome order?
gff3
sort
updated 13 hours ago by
Pierre Lindenbaum
154k • written 15 hours ago by
BioinfoBee
• 0
1
vote
1
reply
241
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 22 hours ago by
GenoMax
129k • written 23 hours ago by
Mohd
▴ 20
0
votes
5
replies
236
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 14 hours ago by
Joe
21k • written 23 hours ago by
gunala.nikhil
• 0
2
votes
2
replies
232
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
12 hours ago by
Chris
▴ 100
4
votes
3
replies
232
views
Optimum setting for local blastp for ~10K sequences
blast
blastp
hpc
updated 13 hours ago by
GenoMax
129k • written 1 day ago by
sodiumnitrate
▴ 20
0
votes
1
reply
229
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 13 hours ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
0
votes
4
replies
222
views
convert data frame with character column to data frame with integer column
r
14 hours ago by
atemedorri137798
• 0
0
votes
1
reply
206
views
News:
7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Variant-Calling
Transcriptomics
RNA-Seq
DNA-Seq
updated 17 hours ago by
Ram
39k • written 26 days ago by
David Langenberger
9.9k
0
votes
5
replies
198
views
All combinations of two columns R
R
updated 17 hours ago by
Ram
39k • written 1 day ago by
Fernando
• 0
1
vote
2
replies
160
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 18 hours ago by
thadjudkins2
• 0 • written 1 day ago by
herh
• 0
5
votes
3
replies
159
views
What does canonical transcript mean in the context of VEP
vep
updated 4 hours ago by
Vincent Laufer
★ 2.9k • written 15 hours ago by
curious
▴ 720
2
votes
4
replies
154
views
bcftools "--filter-logic" flag, what + means?
bcftools
vcf
updated 17 hours ago by
Ram
39k • written 1 day ago by
Eugene A
▴ 170
2
votes
3
replies
145
views
Low mapping percentage
mapping
STAR
RNAseq
28 minutes ago by
Sib
▴ 40
0
votes
1
reply
134
views
Merge different vcf files
vcf
updated 17 hours ago by
Ram
39k • written 1 day ago by
caique.manochio
• 0
0
votes
2
replies
118
views
integrate single cell RNA sequencing data
scRNAseq
single-cell
updated 4 hours ago by
Hamid Ghaedi
2.9k • written 18 hours ago by
Andy
▴ 50
0
votes
3
replies
119
views
hardfilter error
bam
recall
22 hours ago by
bestone
▴ 10
0
votes
1
reply
111
views
how to call variants in haploid genome
haploid-genome
updated 17 hours ago by
Ram
39k • written 1 day ago by
itsmesmb
• 0
0
votes
1
reply
111
views
Creating a local version of Clustered NR database
diamond
clustered-nr
blast
updated 17 hours ago by
Ram
39k • written 1 day ago by
Wilford203
• 0
0
votes
1
reply
105
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 22 hours ago by
raphael.B
▴ 360 • written 1 day ago by
sonsunjirachote
• 0
0
votes
1
reply
94
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
updated 14 hours ago by
GenoMax
129k • written 20 hours ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
84
views
Job:
Postdoctoral Research Associate in bio-ontologies and machine learning (Imageomics)
Machine-Learning
PostDoc
Data-Science
Biology
Ontology
updated 14 hours ago by
Ram
39k • written 15 hours ago by
Jim
• 0
0
votes
1
reply
82
views
Why is coordinate sort required before findng read depths?
wgs
sambamba
updated 15 hours ago by
Ram
39k • written 16 hours ago by
guntul
• 0
0
votes
0
replies
77
views
NMDS plotting issue
NMDS
metagenomic
20 hours ago by
arshad1292
▴ 90
1
vote
0
replies
74
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 17 hours ago by
Ram
39k • written 22 hours ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
70
views
News:
Generalized Linear Models (GLM) course in R
R
GLM
statistics
20 hours ago by
carlopecoraro2
★ 2.3k
0
votes
0
replies
68
views
busco id description
OrthoDB
BUSCO
updated 18 hours ago by
Ram
39k • written 19 hours ago by
hembrom.angelina
• 0
0
votes
0
replies
67
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
14 hours ago by
Mark
• 0
0
votes
0
replies
66
views
IGV insertions
insertions
IGV
21 hours ago by
christoph.schubart
• 0
0
votes
0
replies
65
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 23 hours ago by
GenoMax
129k • written 23 hours ago by
Dablax
• 0
0
votes
0
replies
63
views
jellyfish options
kmer
jellyfish
22 hours ago by
Tele
• 0
156 results • Page
3 of 4
Recent Votes
Comment: Low mapping percentage
Comment: Low mapping percentage
A: genomicranges outside sequence bounds
A: how can i download human ribosomal reference ?
Bayesian network for biological data using bnlearn
Comment: What does canonical transcript mean in the context of VEP
Answer: What does canonical transcript mean in the context of VEP
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Recent Replies
Comment: Low mapping percentage
by
Sib
▴ 40
Thank you for the reply. If there is not much I can do about the contamination at this stage, what is the benefit of knowing the source of…
Answer: integrate single cell RNA sequencing data
by
Hamid Ghaedi
2.9k
There are different approaches that you may choose to deal with batch correction. Harmony is one of those approaches that has been shown to…
Comment: What does canonical transcript mean in the context of VEP
by
Vincent Laufer
★ 2.9k
@curious - The only thing I have to add to @yokofakun 's precise answer is that, while you are considering and reading about Ensembl canoni…
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Thank you for the instruction! I see the beside json file we also have input file which I am confused. Because we have already defined the …
Comment: Comparing loci across catalogs
by
rycro_c
• 0
Hi @Austin, Did you ever figure this out?
Comment: Low mapping percentage
by
Dave Carlson
★ 1.3k
I've been faced with similar issues in the past. Both option 1 and 2 seem useful. You can also treat your data as accidental metagenomic …
Comment: How to sort gff3 according to chromosome order?
by
Pierre Lindenbaum
154k
-s, --stable stabilize sort by disabling last-resort comparison
Comment: Low mapping percentage
by
GenoMax
129k
If you do have contamination (either from rRNA of same species or from true contaminant(s)) there is not much you can do about that at this…
Comment: Optimum setting for local blastp for ~10K sequences
by
GenoMax
129k
> Running the same sequence on the blast web server took 10 seconds Don't try to compare anything local with NCBI's web blast infrastruct…
Comment: how to Construct a Newick tree file from five large fasta files
by
Joe
21k
Yes, I know - but that doesn't answer the question. **What *kind* of phylogenetic tree?**
Comment: Optimum setting for local blastp for ~10K sequences
by
sodiumnitrate
▴ 20
Thank you for the explanation! I managed to get diamond to work, but I'm having trouble getting it to run faster than blast. For a single t…
Comment: What is "pident" (percentage of identical matches) in the "Diamond" protein alig
by
GenoMax
129k
That is the question @Vincent answer poses since it seems to correspond to something different. You can also create an issue on https://gi…
Answer: How to sort gff3 according to chromosome order?
by
GenoMax
129k
Please use `AGAT`: https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html
Comment: convert data frame with character column to data frame with integer column
by
atemedorri137798
• 0
dear @Basti : As you said in order to clarify my issue I edit question box with give an example. I will be grateful if you take a look at …
Comment: How to sort gff3 according to chromosome order?
by
Ram
39k
Those are your options with the `sort` utility - you can either keep the existing order or re-order by coordinate. If you're looking for a …
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