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122,201 results • Page
610 of 2445
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Votes
Replies
6
votes
7
replies
5.4k
views
Biopython SeqIO: AttributeError: 'str' object has no attribute 'id'
filtering
biopython
fasta
python
sequence
updated 4.3 years ago by
Shred
★ 1.6k • written 4.3 years ago by
mdgn
▴ 10
0
votes
2
replies
1.2k
views
Plot assigned / unassigned reads distance to 3'UTR
bedtools
RNA-seq
closest
4.3 years ago by
nlehmann
▴ 150
2
votes
4
replies
2.5k
views
How to compare LD of a gene for all subpopulations in 1000 Genome?
LDPlot
SNPs
variants
1000Genome
4.3 years ago by
Rashmi
▴ 20
3
votes
11
replies
7.9k
views
Converting gene symbols to protein (uniprot) ids gives multiple matches per gene symbol. Why?
Uniprot
r
updated 4.3 years ago by
cpad0112
21k • written 4.4 years ago by
peter.berry5
▴ 60
0
votes
0
replies
1.1k
views
manhattan plot
fst
vcf
manhattan
4.3 years ago by
anithanagaraj93
▴ 10
4
votes
6
replies
1.9k
views
Genome analysis and improvement
genome
4.3 years ago by
Duminda
▴ 10
0
votes
4
replies
3.5k
views
How to modify dot plot in MUMmer 3 for bacteria comparative genomics?
mummerplot
updated 4.3 years ago by
Mensur Dlakic
★ 30k • written 4.3 years ago by
Student
▴ 30
4
votes
4
replies
1.8k
views
Exonerate - issues when running it
Exonerate
4.3 years ago by
helloword
• 0
0
votes
1
reply
874
views
Using FPKM value from the database
gene-expression
FPKM
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
shahbaz.ahmed
▴ 40
0
votes
5
replies
3.9k
views
CellPhoneDB results
CellPhoneDB
statistics
4.3 years ago by
torabian.p
• 0
0
votes
0
replies
756
views
How can I find genomes that have linked transcriptome data ? (bacteria)
bacteria
esearch
ncbi
4.3 years ago by
hugo.avila
▴ 540
4
votes
4
replies
2.2k
views
Extract subject sequences from Blast result
sequence
blast
homology
4.3 years ago by
mnsp088
▴ 100
0
votes
0
replies
788
views
GSEA p value dependent on pre-ranked list size?
gsea
enrichment
p-value
statistics
4.3 years ago by
garfield320
▴ 20
0
votes
0
replies
783
views
Job:
Need bioinformatician at UCSF to study infectious disease & malaria genomic epidemiology & serology
bioinformatician
updated 2.5 years ago by
Ram
45k • written 4.3 years ago by
Teresa.Moeller
• 0
6
votes
4
replies
6.9k
views
Pandas dataframe to H5ad file
H5
python
pandas
4.3 years ago by
roy.granit
▴ 890
0
votes
3
replies
1.9k
views
Missing mappability file for mm10
mm10
mappability
updated 4.3 years ago by
Ram
45k • written 6.4 years ago by
fabbri.marco
▴ 20
0
votes
1
reply
2.8k
views
Clusterprofiler object 'GO2ONT' not found
get_GO_data
go2ont
enrichgo
clusterprofiler
GO
4.3 years ago by
corinne_hutfilz
• 0
0
votes
3
replies
1.6k
views
CreatePHG_step2_consensu
PHGwiki
PHG
updated 4.3 years ago by
pjb39
▴ 220 • written 4.3 years ago by
bp
• 0
0
votes
0
replies
446
views
Can´t create a consensus file from my VCF and reference genome
migrate-n
4.3 years ago by
Dieggar
• 0
1
vote
4
replies
2.3k
views
R package for filtering expression data
gene-expression
r
EMA
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
melissachua90
▴ 70
0
votes
1
reply
1.1k
views
ARACNE Minet R studio
ARACNE
Minet
updated 4.3 years ago by
andres.firrincieli
3.9k • written 4.3 years ago by
ashtay
• 0
0
votes
2
replies
1.1k
views
Should I run GISTIC2.0 for cases/controls separately?
GISTIC2.0
CNV
CNA
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
@e95917ed
• 0
0
votes
1
reply
646
views
Problem for interpreting results of ClusterViz
Cytoscape
updated 4.3 years ago by
Scooter
▴ 310 • written 4.4 years ago by
fahim
▴ 20
0
votes
1
reply
818
views
Cytoscape - How to filter when starting from a complete network, built from a gene-to-gene adjacency matrix
cytoscape
updated 4.3 years ago by
Scooter
▴ 310 • written 4.4 years ago by
JP
▴ 30
0
votes
1
reply
637
views
Cytoscape: GeneMANIA plug-in output.
GeneMANIA
analysis
cytoscape
network
analysis.
updated 4.3 years ago by
Scooter
▴ 310 • written 4.4 years ago by
robynadams
• 0
2
votes
2
replies
1.4k
views
How to use RINalyzer plugin in cytoscape
cytoscape
RINalyzer
networks
updated 4.3 years ago by
Scooter
▴ 310 • written 4.4 years ago by
rohitsatyam102
▴ 940
2
votes
3
replies
2.1k
views
How to plot/combine biological replicates on a genomic features plot for methylated array?
array
methylation
beadchip
plot
features
genomic
updated 4.3 years ago by
Papyrus
★ 3.1k • written 4.3 years ago by
Pratik
★ 1.1k
10
votes
8
replies
8.4k
views
Bcftools how to add DP to FORMAT field (get per sample read depth for REF vs ALT alleles )
bcftools
snp
vcf
calling
updated 4.3 years ago by
Michal Nevo
▴ 140 • written 4.4 years ago by
Linda
▴ 80
11
votes
13
replies
4.2k
views
Why is WGS/WES depth of Y chromosome highly variable?
chromosome-Y
whole-genome-sequencing
updated 2.9 years ago by
Ram
45k • written 4.3 years ago by
samuelandjw
▴ 270
3
votes
7
replies
2.8k
views
How to infer segment direction from vcf
SV
vcf
NGS
4.3 years ago by
octpus616
▴ 120
0
votes
0
replies
1.3k
views
Explanation of generatio from clusterProfiler package
transcriptomic
proteomics
4.3 years ago by
javanokendo
▴ 60
2
votes
5
replies
2.7k
views
Reference file for base recalibration
base
NGS
recalibration
preprocessing
GATK
4.3 years ago by
priya.bmg
▴ 70
5
votes
2
replies
2.8k
views
Calculating minor allele frequency for GnomAD VCF file
gnomAD
genome
updated 4.3 years ago by
Kalin
▴ 50 • written 5.0 years ago by
Jamie Watson
▴ 20
8
votes
5
replies
6.1k
views
Quickly get allele frequencies from Gnomad
gnomad
allele freq
ngs
updated 3.1 years ago by
Kalin
▴ 50 • written 5.3 years ago by
Floydian_slip
▴ 170
4
votes
10
replies
3.7k
views
Help With TCGAbiolinks package
rnaseq
TCGA
tcgabiolinks
R
bioconductor
4.3 years ago by
daniela.paola.s.p
▴ 70
0
votes
4
replies
2.0k
views
How to convert gene names to EC numbers?
database
updated 4.3 years ago by
lieven.sterck
16k • written 4.3 years ago by
dpc
▴ 250
4
votes
3
replies
2.5k
views
RNA-Seq Mapping Genome or Transcriptome
Genome
Transcriptome
Rna-Seq
updated 4.3 years ago by
bigomics.team
▴ 90 • written 4.3 years ago by
santos48
▴ 40
1
vote
0
replies
903
views
Tool:
Omics Playground: visualization and analysis of transcriptomics and proteomics data
proteomics
RNA
RNA-seq
scRNA-seq
omics
data
4.3 years ago by
bigomics.team
▴ 90
0
votes
0
replies
668
views
Biotype assignment for co-expression network
biotype
co-expression
4.3 years ago by
imaparna27
▴ 20
2
votes
5
replies
4.5k
views
collapsing pacbio reads into a single sequence
pacbio
4.3 years ago by
Sara
▴ 280
0
votes
0
replies
969
views
News:
Online training -Metabolomics in R
Metabolomics
4.3 years ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
1.1k
views
Older version of markers from Chocophlan
Chocophlan
Metaphlan
updated 4.3 years ago by
Ram
45k • written 4.3 years ago by
fyfes
▴ 70
2
votes
2
replies
1.7k
views
Mark Duplicates
picard
GATK
NGS
4.3 years ago by
priya.bmg
▴ 70
0
votes
0
replies
675
views
GenomicRatioSet object after minfi normalization does not show method used for preprocessing.
Illumina
minfi
EPIC
R
4.3 years ago by
samuel.carleial
• 0
0
votes
0
replies
1.2k
views
How to interpret scRNA-Seq cell dynamics from scVelo and CytoTrace results
velocyto
cell
cytotrace
rnaseq
dynamics
4.3 years ago by
gundalav
▴ 380
1
vote
2
replies
10k
views
TypeError: must be real number, not dict in python
string
python
dict
updated 4.3 years ago by
Joe
22k • written 4.3 years ago by
Georgia
• 0
3
votes
2
replies
1.7k
views
What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
beadchip
array
methylation
4.3 years ago by
Pratik
★ 1.1k
3
votes
4
replies
1.8k
views
How many reads does Delly use for variant calling?
DNA-seq
bwa-mem
delly
bowtie2
updated 3.6 years ago by
archanaverma433
▴ 10 • written 4.3 years ago by
gt
▴ 30
2
votes
1
reply
2.4k
views
How to filter delly variants?
calling
DNA-seq
delly
variants
updated 4.3 years ago by
trausch
★ 2.0k • written 4.3 years ago by
gt
▴ 30
0
votes
1
reply
755
views
Finding Molecular function for more than 100 GO terms
Gene
Ontology
updated 4.3 years ago by
Pierre Lindenbaum
166k • written 4.3 years ago by
abhilashtripathi10
▴ 20
122,201 results • Page
610 of 2445
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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
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Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
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Answer: Getting the overlap between two GTF files
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Recent Replies
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…
Comment: Midpoint rooting IQTREE newick file moves node support around
by
Luca Arbore
▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets
by
GenoMax
154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets
by
DrSmad
▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets
by
zizigolu
★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
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