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1,000 results • Page 4 of 20
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1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 6 days ago by 10k • written 6.1 years ago by ▴ 10
1
vote
8
replies
2.5k
views
subset data problem
R seurat
9 months ago by Andy ▴ 120
0
votes
2
replies
2.5k
views
Error while running MEGAX
multiple-sequence-alignment MEGAX
updated 11 months ago by 43k • written 5.9 years ago by ▴ 20
5
votes
5
replies
2.4k
views
Quickly retrieve reference genome sequence within python
sequence python
updated 6 months ago by ▴ 20 • written 5.6 years ago by ▴ 20
0
votes
12
replies
2.4k
views
Differential gene expression analysis with no replicates using edgeR
edgeR RNA-seq DEG
updated 4 months ago by ▴ 90 • written 17 months ago by ▴ 280
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq Somatic-Mutation Variant-Calling
updated 4 weeks ago by 43k • written 6.2 years ago by ▴ 600
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 20 months ago by ▴ 20
5
votes
8
replies
2.4k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 15 months ago by • 0
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 11 days ago by 43k • written 4.8 years ago by ▴ 10
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 12 days ago by 43k • written 21 months ago by ▴ 20
2
votes
6
replies
2.4k
views
No best K value found
Assembly Kmergenie
updated 5 months ago by • 0 • written 7.2 years ago by ▴ 80
2
votes
2
replies
2.4k
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 100
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 20 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
2
replies
2.4k
views
Error in Adding 1000Genomes Ancestral Allele info: Using VCF tools fill-aa
vcftools samtools faidx tabix 1000Genomes
updated 11 months ago by ★ 2.1k • written 6.5 years ago by ▴ 10
1
vote
3
replies
2.4k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 5 months ago by ▴ 10 • written 7.5 years ago by 11k
0
votes
0
replies
2.4k
views
Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format
r
updated 10 months ago by 43k • written 10.6 years ago by ▴ 20
1
vote
3
replies
2.3k
views
Use vcf files for dN/dS calculations
sequencing
updated 6 months ago by ▴ 850 • written 6.3 years ago by ▴ 120
2
votes
20
replies
2.3k
views
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
vg
7 months ago by Maxine ▴ 40
2
votes
5
replies
2.3k
views
GTF file for HIV strain pNL4-3
HIV annotation mapping
updated 8 weeks ago by ▴ 140 • written 5.9 years ago by ★ 1.9k
1
vote
0
replies
2.3k
views
Inflated qq plot and genomic inflation est. lambda
gene SNP genome
updated 10 months ago by 43k • written 5.9 years ago by ▴ 130
0
votes
0
replies
2.3k
views
Slimming or not slimming with Gene Ontology: which tool should be used?
gene-ontology go-annotation
updated 10 months ago by 43k • written 7.7 years ago by ▴ 360
2
votes
6
replies
2.3k
views
Basecalling with dorado
variants dorado alignment methylation nanopore
3 months ago by eesiribloom ▴ 80
0
votes
1
reply
2.3k
views
Cochran-Armitage trend test
plink
updated 10 months ago by 43k • written 7.7 years ago by ▴ 30
1
vote
1
reply
2.3k
views
RStudio Cloud : Problem in Package Installing
RStudio Bioconductor
updated 10 months ago by 43k • written 4.0 years ago by • 0
1
vote
1
reply
2.3k
views
Tools for just generating a file including all shared variants in all VCF files
vcf shared-variants
updated 10 months ago by 43k • written 7.7 years ago by ▴ 80
2
votes
2
replies
2.3k
views
bcftools annotate -a
bcftools VCF
updated 10 months ago by 43k • written 14 months ago by ▴ 120
0
votes
11
replies
2.2k
views
i want to convert .ht2 files into FASTA file
GATK HISAT2 FASTA
updated 10 months ago by 43k • written 4.9 years ago by • 0
2
votes
5
replies
2.2k
views
Reciprocal blast commandline
Blast
updated 10 months ago by 43k • written 4.7 years ago by ▴ 30
1
vote
2
replies
2.2k
views
Quantitative anlysis of alternative splicing events
RNA-Seq
updated 10 months ago by 43k • written 9.6 years ago by ▴ 90
0
votes
4
replies
2.2k
views
HOMER load genomes not working
HOMER rna pombe genome
updated 10 months ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
2.2k
views
MACS2 result analysis
peak-calling macs2 ChIP-Seq
updated 10 months ago by 43k • written 4.9 years ago by ▴ 90
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral genome
updated 7 weeks ago by • 0 • written 2.7 years ago by ▴ 310
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 6 months ago by • 0 • written 3.5 years ago by • 0
0
votes
1
reply
2.2k
views
monocle how to identify branches
RNA-Seq pseudotime monocle
updated 10 months ago by 43k • written 5.5 years ago by ▴ 40
1
vote
1
reply
2.2k
views
NS, AC, AN and AF in VCF file
VCF
updated 7 months ago by • 0 • written 21 months ago by ▴ 340
0
votes
5
replies
2.2k
views
error during installationi of KisSplice
cpp c RNA-Seq kissplice SNP
updated 11 months ago by 43k • written 7.7 years ago by • 0
14
votes
18
replies
2.2k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 200 • written 7 months ago by ▴ 260
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 11 days ago by 43k • written 4.7 years ago by ▴ 10
0
votes
2
replies
2.2k
views
ROSE Algorithm for Ranking Super Enhancers
ChIP-Seq
updated 9 weeks ago by 43k • written 3.8 years ago by ▴ 150
0
votes
3
replies
2.2k
views
extraction of original gene iDs from reference annotation file
rna-seq
updated 7 months ago by • 0 • written 5.8 years ago by ▴ 110
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 12 weeks ago by 43k • written 21 months ago by ▴ 10
0
votes
1
reply
2.2k
views
hmmsearch didn't work with nucleotide genome
genome hmmsearch HMMER
updated 10 months ago by 43k • written 6.1 years ago by • 0
0
votes
5
replies
2.2k
views
terminal can't activate base automatically (conda)
conda
updated 11 months ago by 43k • written 2.7 years ago by ▴ 20
3
votes
7
replies
2.2k
views
align_and_estimate_abundance error Trinty
align_and_estimate_abundance RNA-SEQ RSEM Trinity
updated 11 months ago by 43k • written 2.6 years ago by ▴ 60
4
votes
2
replies
2.2k
views
Bfast Match Paired End Reads - Reports Half Total Number Of Reads
paired-end alignment next-gen
updated 10 months ago by 43k • written 11.3 years ago by ▴ 50
0
votes
2
replies
2.1k
views
Need help with error fromTOMplot network heatmap: "Error in x[, iy] : subscript out of bounds"
WGCNA TOMplot
updated 11 months ago by 43k • written 3.1 years ago by • 0
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.0 years ago by ▴ 10
0
votes
5
replies
2.1k
views
Extra header column stopping EMMAX (C), but not seen in input files
emmax genomics Cpp plink GWAS
updated 10 months ago by • 0 • written 6.2 years ago by ▴ 100
0
votes
2
replies
2.1k
views
Tool for manual annotation curation
annotation
updated 10 months ago by 43k • written 6.7 years ago by ★ 1.4k
1,000 results • Page 4 of 20
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
A: Insert Size And Fragment Size ?
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Answer: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Can I merge Hi-C fastq files from different lanes? by GenoMax 141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset? by GenoMax 141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository? by GenoMax 141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2 by GenoMax 141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
Answer: High Malat-1 expression in single cell data by ATpoint 82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing? by GenoMax 141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous by trausch ★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
Thats very intersting! What are the features in your classifier?
Answer: Limma Analysis Agilent Microarray Data (GPL1708) by hagl ▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better? by Lluís R. ★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better? by ATpoint 82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file by marco.barr ▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Comment: Finding batch and outlayers by christopher medway ▴ 450
You could perform an ANOVA to test if there is a significant association between batch number and a given Principal Component
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