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122,200 results • Page 619 of 2444
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4
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6
replies
2.1k
views
Single-End to reduce cost for Differential Expression Analysis ?
expression single-end differential analysis ngs deg
4.4 years ago by Evan ▴ 250
0
votes
0
replies
747
views
Job: ELIXIR-UK FAIR Data Stewardship Training Fellowship
Fellowship
4.4 years ago by Hannah • 0
0
votes
0
replies
1.1k
views
minimap2 Nanopore direct-RNA mapping
rna minimap2 nanopore
4.4 years ago by Gregor Rot ▴ 550
4
votes
6
replies
5.1k
views
How to download NCBI fastq data to local machine where access type is "Use Cloud Data Delivery"
delivery NCBI cloud
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 80
0
votes
2
replies
1.2k
views
VCF file - If format is GT:PL what does 1:161, 0 mean for GT column
bcftools vcf
4.4 years ago by Linda ▴ 80
0
votes
0
replies
757
views
Best way of visualising genetic variation for publication in a gene with many exons
graphs snv lollipop snp Visualisation
4.4 years ago by tacrolimus ▴ 150
0
votes
0
replies
748
views
How to simulate a null distribution of paralog ages without ancient WGDs to use in K-S goodness-of-fit test
WGD distributions plots age KS gene
4.4 years ago by Emily Wasson ▴ 30
2
votes
2
replies
1.1k
views
What are DNA-related genes?
gen
updated 4.4 years ago by ★ 2.2k • written 4.5 years ago by • 0
0
votes
0
replies
665
views
SPARQL query help
genes SPARQL R
4.4 years ago by flalom • 0
0
votes
1
reply
902
views
P-value calculation for DNA motifs
python Genomics DNA R
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 160
9
votes
6
replies
2.5k
views
Genotype meaning
genotype BL21
4.4 years ago by A_heath ▴ 180
3
votes
7
replies
13k
views
understanding log2fold change of 0.31 and -0.25
rnaseq log2FC
4.4 years ago by arshad1292 ▴ 110
0
votes
6
replies
2.5k
views
How to get genes list from goana function in R
R
4.4 years ago by smrutimayipanda ▴ 20
0
votes
0
replies
759
views
Measuring pairwise distances between pockets in structural alignment
biopython protein alignment distance pairwise
4.4 years ago by Jonathan Lefebre ▴ 70
0
votes
2
replies
1.0k
views
No support values on ASTRAL when I group the different specimens into species groups
multi-species ASTRAL ILS coalescent model
4.4 years ago by Konstantinos • 0
0
votes
0
replies
651
views
If a gene has geater number of Transcription Factor Binding Sites ?
TFBS Gene Transcription sites binding regulation
4.4 years ago by iqra • 0
2
votes
5
replies
3.1k
views
Using the same cutoff on peak calling?
macs2 cutoff
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 20
0
votes
0
replies
658
views
Is it possible to change values ​​to data before vsn applied?
genetic bio vsn R
4.4 years ago by dxodnd • 0
0
votes
0
replies
824
views
R is saving empty sheets for several KM plots using RTCGA package
RTCGA R
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 390
1
vote
3
replies
1.9k
views
Extremely high adapter content and low alignment rate in RNAseq
alignment adapter RNAseq
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 300
3
votes
2
replies
1.9k
views
Raw counts of scRNA-seq
scRNA-seq
updated 4.4 years ago by ★ 8.6k • written 4.4 years ago by ★ 4.4k
1
vote
3
replies
1.4k
views
Pathway Analysis Interpretation
analysis kegg pathway rna-seq
updated 4.4 years ago by ▴ 390 • written 4.4 years ago by • 0
0
votes
1
reply
2.2k
views
Generating a dotplot following ragtag scaffolding
ragtag dotplot mummerplot genome assembly
updated 4.4 years ago by ▴ 640 • written 4.4 years ago by • 0
1
vote
1
reply
1.6k
views
MAESTRO returns an error
CIBERSORT scRNA-seq MAESTRO RNA-seq single-cell
4.4 years ago by Luna_P ▴ 20
0
votes
2
replies
1.2k
views
How to retrieve a specific version of Araport annotation file?
Arabidopsis gtf annotations
4.4 years ago by Hojn ▴ 30
0
votes
2
replies
3.5k
views
stats file in Mutect2 calling
gatk
updated 4.4 years ago by ▴ 70 • written 6.2 years ago by ▴ 20
0
votes
0
replies
712
views
The P-value histogram when using the option lfcThreshold > 0
DESeq2 lfcThreshold
4.4 years ago by haasroni • 0
0
votes
8
replies
5.5k
views
Poly-G in head of read NovaSeq
sequencing
updated 4.4 years ago by • 0 • written 5.4 years ago by ▴ 100
5
votes
7
replies
2.1k
views
What does "viewpoint" mean?
definition
4.4 years ago by ccc ▴ 30
0
votes
0
replies
820
views
error related to MetaXcan
PrediXcan TWAS MetaXcan SNP
4.4 years ago by rheab1230 ▴ 150
0
votes
3
replies
1.8k
views
Comparison of two populations of scRNAseq cells
scRNA-seq RNA-seq compare single-cell
updated 4.4 years ago by ★ 19k • written 4.4 years ago by • 0
2
votes
1
reply
848
views
Handling RNA-seq samples from the same individual in DEseq2 analysis
DEseq2 RNA-seq
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 10
4
votes
1
reply
1.2k
views
Covariates didn't change GWAS too much?
Covariates GWAS MixedLinearModel MLM LMM
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by ▴ 40
0
votes
0
replies
1.8k
views
Job: CDC Bioinformatics position
CDC bash python git
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
2
votes
0
replies
890
views
Job: Bioinformatics Positions at the Penn Epigenetics Institute
imaging UPENN genomics epigenetics
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 40
1
vote
5
replies
2.3k
views
Preparing CHASMplus database for annotation
ANNOVAR CHASM CHASMplus annotation
updated 4.4 years ago by ▴ 1000 • written 4.4 years ago by ▴ 110
0
votes
1
reply
1.3k
views
Average duplicate read rate in a 'typical' RNA-seq experiment
RNA-seq
updated 4.4 years ago by 90k • written 4.4 years ago by ▴ 80
0
votes
4
replies
1.5k
views
Problem facing for retrieving Phalanx_id from geo data set in R
Phalanx_id GEO dataset
4.4 years ago by fahim ▴ 20
0
votes
0
replies
1.4k
views
Calculate significance (P values) of Fst values
fst p-value genotype
updated 2.9 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
5
replies
2.1k
views
Is it possible to remove overrepresented sequence from trimgalore?
RNA-SEQ
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
0
votes
2
replies
1.3k
views
Shannon Diversity at the gene level
Shannon Diversity Alpha
updated 4.4 years ago by 22k • written 4.4 years ago by • 0
2
votes
3
replies
1.4k
views
Contigs and scaffold in reference genome
BWA Ensembl Genome Reference HiSat NCBI
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 550
0
votes
2
replies
1.7k
views
Identify most and least abundant allele (nMAJ and nMIN) for pooled heterozygosity (hp) analysis from vcf file
selection wgs vcf gatk
updated 4.1 years ago by ▴ 150 • written 4.4 years ago by ▴ 940
1
vote
1
reply
1.3k
views
The P-values with lfcShrink and ashr shrinkage estimator
DESeq2 ashr
updated 4.4 years ago by 90k • written 4.4 years ago by • 0
0
votes
1
reply
847
views
Statistical analysis, such as SNPs association, of pooled-seq data
Pooled NGS SNP GWAS
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
1
vote
1
reply
1.1k
views
What is the meaning of mRNA_start_NF for a lncRNA transcript?
annotation gencode genome
updated 4.4 years ago by 24k • written 4.4 years ago by • 0
0
votes
0
replies
1.9k
views
The memory is not enough when run cellranger to align the fq using the two parameters --localcores and --localmem
cellranger 10x
4.4 years ago by whaiyu06 ▴ 80
13
votes
8
replies
19k
views
7 follow
Create Vcf File From A Multiple Sequence Alignments
alignment vcf variant snp
updated 4.4 years ago by ▴ 60 • written 13.4 years ago by ★ 1.6k
3
votes
2
replies
3.5k
views
Where do I share a single-cell dataset?
store share data single-cell
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ★ 1.2k
0
votes
0
replies
568
views
Cell metabolic activity assay - Dose Response Analysis
Analysis R IC50 EC50 DoseResponse
updated 4.4 years ago by 56k • written 4.4 years ago by ▴ 20
122,200 results • Page 619 of 2444
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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
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
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)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
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