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122,202 results • Page
680 of 2445
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0
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News:
Online Training - Conservation Genomics
Genome
Genomics
ConservationGenomics
SNPs
4.5 years ago by
Physalia-courses
★ 2.7k
2
votes
1
reply
1.7k
views
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
rna
splice-junction
vcf
4.6 years ago by
William
★ 5.4k
0
votes
3
replies
1.6k
views
How to find single copy family from InParanoid output
InParanoid
single
copy
updated 4.6 years ago by
Dunois
★ 2.9k • written 4.6 years ago by
gengyang12138
▴ 20
0
votes
0
replies
1.7k
views
No peaks found in Signac's FindMarker
seurat
atac-seq
Signac
atac
singlecell
4.6 years ago by
ahmad mousavi
▴ 800
6
votes
4
replies
1.7k
views
Concatenating fasta files based on prefix ?
aligment
RNA
DNA
fasta
updated 4.6 years ago by
5heikki
11k • written 4.6 years ago by
sunnykevin97
▴ 1000
15
votes
10
replies
4.7k
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript
rna-seq
updated 4.6 years ago by
tamerg
▴ 100 • written 4.6 years ago by
Quanyou
• 0
0
votes
2
replies
1.1k
views
Database/list of disease complications
complications
database
disease
updated 4.6 years ago by
ellimilial
▴ 20 • written 4.6 years ago by
Nur
• 0
0
votes
2
replies
1.8k
views
Is it possible to annotate a file for the human genome using the command line without using an amino acid sequence
Annotation
human
DNA
PROVEAN
4.6 years ago by
kamanovae
▴ 100
1
vote
0
replies
1.1k
views
braker2 output: gff file is missing and species folder is empty
prothint
braker2
genome
braker
annotation
updated 4.6 years ago by
zx8754
12k • written 4.6 years ago by
praasu
▴ 40
0
votes
2
replies
1.3k
views
Does GISAID fasta files contain spike protein or whole genome sequence?
sequence
protein
spike
genome
updated 4.6 years ago by
WouterDeCoster
48k • written 4.6 years ago by
er.alruba2017
• 0
2
votes
0
replies
1.1k
views
Job:
ELIXIR Training Coordinator (pan-European bioinformatics training)
training
lifescience
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
Erin Haskell
▴ 470
1
vote
4
replies
2.1k
views
Why GC content is important on NIPT results?
NGS
NIPT
Sequencing
4.6 years ago by
khanhlpbao
• 0
1
vote
4
replies
2.4k
views
Variant calling from comparison of assembled genomes where there is only one read depth.
variant
updated 4.6 years ago by
samuel.a.odonnell
▴ 640 • written 4.6 years ago by
Hans
▴ 150
3
votes
2
replies
1.6k
views
Finding all instances of a recurring motif in a repeat protein
repeat
markov
alignment
motifs
4.6 years ago by
NeuralCode
▴ 10
0
votes
0
replies
583
views
rpy hgu133a.db loading error
hgu133a.db
python
rpy
4.6 years ago by
dxodnd
• 0
4
votes
4
replies
4.2k
views
Help with CNV calling using ExomeDepth
exomedepth
R
CNV
gCNV
exome
updated 4.6 years ago by
Joakim
▴ 50 • written 5.0 years ago by
luffy
▴ 130
2
votes
1
reply
1.2k
views
How to grep scaffold from the vcf file
introns
VCF
scaffolds
updated 4.6 years ago by
Pierre Lindenbaum
166k • written 4.6 years ago by
Kumar
▴ 170
0
votes
1
reply
1.1k
views
For loop - mkdir and command
bash
updated 2.4 years ago by
Ram
45k • written 4.6 years ago by
jellila
• 0
2
votes
6
replies
4.2k
views
why my volcano plot looks strange?
wilcox.test
RNAseq
Metabolomics
LCMS
updated 4.6 years ago by
cpad0112
21k • written 4.6 years ago by
hellocita
▴ 40
0
votes
3
replies
6.9k
views
How to interpret multiqc report
QC
multiqc
rna-seq
updated 4.6 years ago by
Phil Ewels
★ 1.5k • written 4.6 years ago by
gt
▴ 30
5
votes
2
replies
2.3k
views
Can you suggest any journal without any publication fee for publishing microbiology and bioinformatics papers?
journals
microbiology
publications
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
saiki
▴ 20
3
votes
1
reply
1.4k
views
How to get all microRNA target genes?
miRNA
multimir
microRNA
targetgenes
tarbase
updated 4.6 years ago by
i.sudbery
22k • written 4.6 years ago by
Katarina
▴ 10
1
vote
3
replies
3.6k
views
vcftools intersect vs bedtools intersect
bedtools
vcf
vcftools
updated 4.3 years ago by
Ram
45k • written 4.6 years ago by
gpen
• 0
2
votes
4
replies
4.7k
views
How to extract sequences from fasta that have a certain length ?
minlength
fasta
updated 4.6 years ago by
shenwei356
8.7k • written 4.6 years ago by
v.berriosfarias
▴ 140
2
votes
5
replies
1.5k
views
Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor
MA
RNA-seq
DESEQ2
4.6 years ago by
raisamathenge
▴ 30
0
votes
5
replies
5.5k
views
How to highlight DE genes in plotMD ?
edgeR
plotMD
volcanoplot
mirnaseq
updated 4.6 years ago by
raulgcova97
• 0 • written 7.6 years ago by
Björn
▴ 110
15
votes
7
replies
2.5k
views
6 follow
Forum:
What to put in my Github
Github
updated 4.6 years ago by
Carambakaracho
★ 3.3k • written 4.6 years ago by
vigbr
▴ 20
0
votes
0
replies
697
views
What criteria follow in order to choose the crystaline structure of a molecule
Molecular
Docking
4.6 years ago by
roybatty269
• 0
2
votes
2
replies
1.7k
views
Recombination maps for cattle
SNP
IMPUTE2
genome
Assembly
updated 4.6 years ago by
Azwan
• 0 • written 6.2 years ago by
mdyogolos
▴ 10
2
votes
2
replies
1.6k
views
Samtools view filter by reference sequence
samtools
4.6 years ago by
maxrwjones
▴ 60
0
votes
0
replies
709
views
The effect of heterozygosity on genome alignment
heterozigosity
alignment
bwa
sequence
4.6 years ago by
Iseez
• 0
0
votes
2
replies
2.4k
views
Segmentation fault (core dumped) error in MUSCLE
NGS
alignment
fastq
linux
sequence
4.6 years ago by
steel1990
▴ 20
0
votes
1
reply
710
views
Genome sequencing data analysis and assembly L.lactis subsp.lactis strain Lac3
well
updated 4.6 years ago by
Mensur Dlakic
★ 30k • written 4.6 years ago by
ipb727258
• 0
4
votes
1
reply
1.1k
views
Is it bad practice to change threshold for interaction probability?
STRING
Cytoscape
updated 4.6 years ago by
Carlo Yague
9.0k • written 4.6 years ago by
gemmalouisebaldock
▴ 20
7
votes
8
replies
3.3k
views
bedops wig2bed 'Row begins with a tab or space' error
wig2bed
bedops
convert2bed
updated 4.6 years ago by
Alex Reynolds
36k • written 4.6 years ago by
a_bis
▴ 40
0
votes
2
replies
1.1k
views
correlation analysis of a single variable versus multiple variables
correlation
r
RNA-Seq
4.6 years ago by
pinheirofabiano
▴ 130
1
vote
0
replies
685
views
Holistic enzyme activity determination with computation
proteomics
protein
enzymes
updated 4.4 years ago by
Ram
45k • written 4.6 years ago by
birbronald9
▴ 10
0
votes
5
replies
1.5k
views
transcription factor activation order
transcription
updated 4.6 years ago by
ATpoint
90k • written 4.6 years ago by
kenny
• 0
0
votes
0
replies
580
views
JoinMap4 makes a new map every time
joinmap
linkage_mapping
genetic_map
SNP
4.6 years ago by
Beetle Editor
• 0
0
votes
3
replies
3.5k
views
LDSC -Genetic correlation, some results all have NA valuies
correlation
ldsc
genetic
gwas
updated 4.6 years ago by
Sam
★ 4.8k • written 4.6 years ago by
d.s.zimmerman
• 0
0
votes
4
replies
2.3k
views
Can Meta-GWAS summary statistic results be used for Meta-GWAS (For example, METAL)?
METAL
input
Meta-analysis
Meta-GWAS
4.6 years ago by
li
• 0
4
votes
6
replies
2.1k
views
Batch effect correction of 2 studies with different covariates
batch-effect
R
RNA-seq
updated 4.6 years ago by
Dunois
★ 2.9k • written 4.6 years ago by
Geo
▴ 20
1
vote
2
replies
1.7k
views
MemoryError w/ matrix | Smith-Waterman Algorithm Python
Python
Smith-Waterman
updated 20 months ago by
Ram
45k • written 4.6 years ago by
Anonymous
▴ 10
0
votes
0
replies
1.2k
views
Job:
Informatician / Data Analyst | University of Glasgow
data-analyst
updated 2.5 years ago by
Ram
45k • written 4.6 years ago by
dariober
15k
1
vote
3
replies
2.2k
views
IndexError: list assignment index out of range | Needleman-Wunsch Algorithm - Python
Python
Needleman-Wunsch
Dynamic-Programming
updated 20 months ago by
Ram
45k • written 4.6 years ago by
Anonymous
▴ 10
1
vote
2
replies
1.9k
views
Pooling normal data in Mutect2
mutect2
pooling
normal
samples
panelofnormals
4.6 years ago by
Michelle
• 0
17
votes
4
replies
6.2k
views
How to extract all columns of CSQ using split-vep plugin of bcftools?
plugin
samtools
bcftools
vcf
split-vep
updated 3.2 years ago by
amy__
▴ 250 • written 4.6 years ago by
DareDevil
★ 4.5k
0
votes
0
replies
1.1k
views
integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
4.6 years ago by
ramyak1912
• 0
3
votes
4
replies
2.1k
views
how to extract REF and ALT DNA string around SNV
SNV
motif
4.6 years ago by
shangguandong1996
▴ 30
0
votes
0
replies
625
views
Minimum enrichment score to take for analysis
Sequencing
Rna-Seq
4.6 years ago by
ashwing.kofficial
▴ 10
122,202 results • Page
680 of 2445
Recent Votes
Comment: low quality data or file name swapping -- cellranger arc errors when processing
Comment: low quality data or file name swapping -- cellranger arc errors when processing
A: Regarding Microarray Platforms
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read
by
cmdcolin
★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets
by
GenoMax
154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Wu-Sheng Zhang
• 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
samuel.a.odonnell
▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
thomas.heigl.ibk
▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing
by
Arup Ghosh
3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
by
Pierre Lindenbaum
166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome?
by
alexandrakortsi
• 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding
by
xinguok794
▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics
by
Kent
▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
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