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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 22 days ago by 10k • written 6.2 years ago by ▴ 10
2
votes
1
reply
2.5k
views
Converting blastn output to VCF (for SNPs): what is the quickest way?
VCF blast SNP xml
updated 10 months ago by 43k • written 6.0 years ago by ★ 3.6k
1
vote
1
reply
2.5k
views
problem with updating trinity
software-error trinity
updated 10 months ago by 43k • written 5.5 years ago by • 0
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg Giraffe calling structural variant
updated 9 months ago by ▴ 460 • written 16 months ago by • 0
0
votes
0
replies
2.5k
views
Analysis and tools for gene/pathway conservation
evolution
updated 11 months ago by 43k • written 9.1 years ago by ▴ 90
4
votes
6
replies
2.5k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 11 months ago by • 0 • written 21 months ago by ▴ 20
0
votes
2
replies
2.5k
views
Error while running MEGAX
multiple-sequence-alignment MEGAX
updated 12 months ago by 43k • written 6.0 years ago by ▴ 20
2
votes
6
replies
2.5k
views
Basecalling with dorado
variants dorado alignment methylation nanopore
4 months ago by eebloom ▴ 80
5
votes
5
replies
2.5k
views
Quickly retrieve reference genome sequence within python
sequence python
updated 6 months ago by ▴ 20 • written 5.6 years ago by ▴ 20
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 28 days ago by 43k • written 21 months ago by ▴ 20
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq Somatic-Mutation Variant-Calling
updated 7 weeks ago by 43k • written 6.2 years ago by ▴ 610
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
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 27 days ago by 43k • written 4.9 years ago by ▴ 10
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 12 days ago by 142k • written 4.5 years ago by ▴ 20
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 5 weeks ago by 43k • written 3.7 years ago by ▴ 20
2
votes
20
replies
2.4k
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
8 months ago by Maxine ▴ 40
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 6.6 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
1
vote
3
replies
2.4k
views
Use vcf files for dN/dS calculations
sequencing
updated 7 months ago by ▴ 860 • written 6.4 years ago by ▴ 120
0
votes
0
replies
2.4k
views
Tool To Convert Affy Oncoscan Data Into Affy Snp6.0 Format
r
updated 11 months ago by 43k • written 10.6 years ago by ▴ 20
2
votes
5
replies
2.4k
views
GTF file for HIV strain pNL4-3
HIV annotation mapping
updated 10 weeks ago by ▴ 140 • written 5.9 years ago by ★ 1.9k
2
votes
2
replies
2.3k
views
bcftools annotate -a
bcftools VCF
updated 10 months ago by 43k • written 14 months ago by ▴ 120
1
vote
1
reply
2.3k
views
RStudio Cloud : Problem in Package Installing
RStudio Bioconductor
updated 11 months ago by 43k • written 4.0 years ago by • 0
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 7.8 years ago by ▴ 360
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 6.0 years ago by ▴ 130
0
votes
1
reply
2.3k
views
Cochran-Armitage trend test
plink
updated 10 months ago by 43k • written 7.8 years ago by ▴ 30
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 210 • written 7 months ago by ▴ 280
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 11 months ago by 43k • written 7.8 years ago by ▴ 80
2
votes
5
replies
2.3k
views
Reciprocal blast commandline
Blast
updated 10 months ago by 43k • written 4.8 years ago by ▴ 30
0
votes
11
replies
2.3k
views
i want to convert .ht2 files into FASTA file
GATK HISAT2 FASTA
updated 10 months ago by 43k • written 5.0 years ago by • 0
1
vote
1
reply
2.3k
views
NS, AC, AN and AF in VCF file
VCF
updated 8 months ago by • 0 • written 22 months ago by ▴ 340
0
votes
2
replies
2.3k
views
ROSE Algorithm for Ranking Super Enhancers
ChIP-Seq
updated 12 weeks ago by 43k • written 3.9 years ago by ▴ 150
0
votes
4
replies
2.3k
views
HOMER load genomes not working
HOMER rna pombe genome
updated 11 months ago by 43k • written 3.9 years ago by • 0
0
votes
7
replies
2.2k
views
Command not found after pip install spliceai
software error
updated 7 months ago by • 0 • written 3.5 years ago by • 0
1
vote
2
replies
2.2k
views
Quantitative anlysis of alternative splicing events
RNA-Seq
updated 10 months ago by 43k • written 9.7 years ago by ▴ 90
0
votes
3
replies
2.2k
views
ANGeS - Ancestral Genome reconstruction
ancestral genome
updated 9 weeks ago by • 0 • written 2.7 years ago by ▴ 310
0
votes
1
reply
2.2k
views
MACS2 result analysis
peak-calling macs2 ChIP-Seq
updated 10 months ago by 43k • written 5.0 years ago by ▴ 90
4
votes
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 3 months ago by 43k • written 21 months ago by ▴ 10
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 27 days ago by 43k • written 4.7 years ago by ▴ 10
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 7.8 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 5.6 years ago by ▴ 40
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 5.9 years ago by ▴ 110
0
votes
3
replies
2.2k
views
minimap's SAM file MAPQ value for the unique alignments
minimap MAPQ RNAseq
11 months ago by Mo ▴ 40
0
votes
1
reply
2.2k
views
hmmsearch didn't work with nucleotide genome
genome hmmsearch HMMER
updated 10 months ago by 43k • written 6.2 years ago by • 0
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
2
votes
13
replies
2.2k
views
RepeatMasker error when trying to generate repeat sequence distribution pie chart (all code and errors provided)
repeatmasker
updated 7 months ago by 43k • written 9 months ago by • 0
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.1 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
Comment: Genome Visualization Tools
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
A: Best de novo assembler for insect genome ?
Comment: sci-RNA-seq
The Biostar Herald for Monday, May 13, 2024
Answer: Finding variants within a subset of a BAM file
Answer: Extracting only 4-fold degenerate sites from gene sequences/alignments?
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Recent Replies
Comment: Genome Visualization Tools by dlera.lozano • 0
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat by Mensur Dlakic ★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Comment: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
Comment: Where to get the following bed file? by wyuan37 • 0
Thanks! Super helpful.
Answer: Post-imputation QC for input into GWAS analyses by LauferVA 4.2k
1. Imputation algorithms will output log files indicating, among other things, accuracy of imputation. We can't comment on specifics as we …
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by GenoMax 142k
You can simply ignore read 2. It is not adding any information since your small RNA's are going to be small and were completely sequenced b…
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
does this work with a single .bed file?
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