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1,000 results • Page 5 of 20
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0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf dna vcf ensembl ngs
updated 5 months ago by • 0 • written 15 months ago by ▴ 30
0
votes
7
replies
475
views
1000 Genome: Cause of duplicate variants with different genotypes
CrossMap 1000Genome 1000G
updated 3 months ago by ▴ 400 • written 3 months ago by ▴ 210
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
1
vote
7
replies
823
views
What could be the rage for Average Coverage after Assembly
viral-genome spades coverage de-novo-assembly
updated 10 months ago by 43k • written 10 months ago by ▴ 70
3
votes
7
replies
381
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc cutadapt illumina tile paired-end
14 days ago by salias • 0
3
votes
7
replies
1.4k
views
Find 3'UTRs for species
Assembly alignment
updated 11 months ago by 43k • written 4.7 years ago by ▴ 110
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
0
votes
7
replies
1.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 11 months ago by 4.2k • written 11 months ago by ▴ 40
0
votes
7
replies
932
views
Tool for Iterative mapping
read-mapping
updated 10 months ago by 43k • written 4.1 years ago by ▴ 10
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
1
vote
7
replies
4.1k
views
Adjust width of annotations in pheatmap
R heatmap
updated 7 months ago by 88k • written 5.5 years ago by ▴ 30
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 11 months ago by 43k • written 5.4 years ago by ★ 2.6k
1
vote
7
replies
922
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19 Mutect2 GATK Variant-Calling
updated 6 weeks ago by 43k • written 9 months ago by ▴ 100
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 4 weeks ago by 43k • written 6.5 years ago by ▴ 10
4
votes
7
replies
1.5k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 142k • written 9 months ago by • 0
0
votes
7
replies
1.4k
views
fasterq-dump outputs "Cannot use '--ngc' as ngc file."
snakemake sra-tools SRA
updated 10 months ago by 43k • written 12 months ago by ▴ 80
0
votes
7
replies
464
views
Salmon Quantification in Alignment based-mode
Salmon RNA-seq TPM
updated 6 weeks ago by 142k • written 6 weeks ago by • 0
5
votes
7
replies
972
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 11 months ago by • 0 • written 4.4 years ago by ▴ 50
1
vote
7
replies
844
views
alignment tool for big data
sequence
updated 10 months ago by 43k • written 4.6 years ago by ▴ 20
5
votes
7
replies
862
views
About the value in bigwig file
ATAC-seq
updated 10 months ago by ▴ 900 • written 10 months ago by ▴ 280
0
votes
7
replies
2.9k
views
qPCR: Huge variation in fold change of genes between biological replicates
qpcr fold-change
updated 8 months ago by 43k • written 5.9 years ago by ▴ 80
3
votes
7
replies
512
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
9 weeks ago by Fadlilah ▴ 10
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 27 days ago by 43k • written 7.7 years ago by ▴ 70
7
votes
7
replies
618
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
1
vote
7
replies
508
views
Question regarding WGCNA
WGCNA Network-construction
4 days ago by deepak • 0
2
votes
7
replies
1.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency gnomad annovar
updated 7 months ago by 43k • written 7 months ago by • 0
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
3
votes
7
replies
531
views
How does kallisto handle multi mapped reads?
kallisto
updated 11 weeks ago by ★ 6.0k • written 11 weeks ago by ▴ 150
4
votes
7
replies
788
views
Alternative for grep in a for loop
linux
updated 7 months ago by 43k • written 7 months ago by ▴ 20
2
votes
7
replies
875
views
Should we assume UMI-based scRNAseq data is not compositional?
compositional scRNAseq
9 months ago by cwwong13 ▴ 40
2
votes
7
replies
664
views
Maker: Combining Annotations for Large Genomes
Maker Genome annotation
12 weeks ago by Kinoppy • 0
0
votes
7
replies
662
views
Using Primer3 with python to genotype a SNP at a particular position
primer3 python position primer
updated 5 months ago by 161k • written 6 months ago by • 0
0
votes
7
replies
1.9k
views
monocle single cell differential expression: error message for HSMM <- estimateDispersions(HSMM) command
single-cell monocle
updated 10 months ago by 3.9k • written 2.3 years ago by ▴ 40
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
12 months ago by sohail.mbio • 0
0
votes
7
replies
1.1k
views
Tool-Compare Sequences within a Single Tree.
mutations sequence alignment
updated 10 months ago by 43k • written 5.2 years ago by • 0
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
4
votes
7
replies
840
views
SNP IDs
SNP
6 months ago by kl ▴ 10
2
votes
7
replies
1.8k
views
Technology Stack of NCBI (Genbank, GEO, etc.)
sequence ncbi gene genbank
updated 11 months ago by 43k • written 6.2 years ago by ▴ 70
4
votes
7
replies
2.7k
views
low bootstrap value?
phylogeny genome alignment
updated 11 months ago by 43k • written 4.9 years ago by ▴ 120
2
votes
7
replies
535
views
How to predication/annotation trans-splicing in genome
trans-splicing genome annotation mitochondrial
3 months ago by oasiswho • 0
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe vg
updated 10 months ago by ▴ 460 • written 10 months ago by • 0
5
votes
7
replies
3.2k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 7 months ago by 100k • written 5.9 years ago by ▴ 10
1
vote
7
replies
1.9k
views
Filtering a VCF by "IMP" flag in INFO with bcftools
vcf bcftools
updated 10 months ago by 43k • written 19 months ago by ▴ 40
1
vote
7
replies
1.6k
views
cannot execute binary file: Exec format error
linux
updated 9 months ago by 54k • written 9 months ago by • 0
0
votes
7
replies
932
views
Mugsy error -directory must be a directory
Mugsy
updated 7 months ago by 43k • written 3.5 years ago by ▴ 160
0
votes
7
replies
546
views
SNP calling with many samples using bcftools
bcftools SNP multithreading
6 months ago by George ▴ 10
0
votes
7
replies
735
views
error MarkerScanner.pl
amphora2
updated 5 months ago by 43k • written 5 months ago by • 0
2
votes
7
replies
938
views
Removing duplicates
duplicates ONT minimap2
updated 25 days ago by ▴ 580 • written 27 days ago by • 0
2
votes
7
replies
584
views
Need a link to OLDERADO server
pdb protein nmr structure
8 weeks ago by b2003 • 0
0
votes
7
replies
532
views
Using VEP annotation output as the input for a second VEP annotation
VCF VEP Annotation
updated 8 weeks ago by 43k • written 3 months ago by • 0
1,000 results • Page 5 of 20
Recent Votes
A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
Answer: Is there any way to modify this pie chart ?
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
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Recent Replies
Comment: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: CNVkit for somatic copy number detection by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object by ATpoint 82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error by trkfs • 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio? by Lukas • 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Answer: How to access GWAVA software of data by nonaddldy ▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Answer: How to access GWAVA software of data by nonaddldy ▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by IdaHao0921 • 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object by Alex Reynolds 35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment by ATpoint 82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation by ATpoint 82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data by ATpoint 82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
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