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Error when converting hmmsearch output to gff file
hmmer2gff gff hmmer
2.4 years ago by v.berriosfarias ▴ 140
1
vote
2
replies
1.2k
views
Difference between variants called in sequences with 2-channel SBS and 4-channel SBS
sbs snp illumina sequence ngs
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 40
0
votes
1
reply
1.3k
views
Can we get fastq read id of certain species that kraken assigned?
taxonomy kraken metagenomic bacteria
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
2
votes
5
replies
2.2k
views
Removing indels in VCF file
bcftools
updated 12 months ago by ▴ 130 • written 2.4 years ago by ▴ 120
0
votes
3
replies
857
views
Merging groups of 1 dataset in R
dataset merge microarray
updated 2.4 years ago by ★ 2.1k • written 2.4 years ago by • 0
0
votes
0
replies
2.3k
views
News: GWAS course
GWAS R
updated 2.4 years ago by 45k • written 2.4 years ago by ★ 2.6k
1
vote
1
reply
867
views
error when converting hmmer table to off table
hmmer2gff gff hmmer
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 140
2
votes
4
replies
3.6k
views
InferCNV how to choose the right reference?
CTC inferCNV reference CNV
updated 2.4 years ago by ▴ 10 • written 4.1 years ago by ▴ 10
0
votes
1
reply
1.3k
views
How to convert a GBFF GFF to GTF
scRNA gff gtf
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
3
replies
1.3k
views
How to extract regions from BAM file on remote server and visualize long-read alignments in IGV?
bam igv
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
0
votes
1
reply
1.9k
views
how to input bedpe file in IGV
IGV interaction input bedpe
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 150
8
votes
9
replies
3.8k
views
Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st intron, ..., 3'UTR, intergenic, ...`
BAM
2.4 years ago by Dan ▴ 180
1
vote
2
replies
983
views
Metadata for oligo bioconductor package
bioconductor microarray metadata oligo R
updated 15 months ago by • 0 • written 2.4 years ago by • 0
0
votes
2
replies
1.8k
views
filtering sniffles variants for precise calls
sniffles vcf variation
2.3 years ago by eebloom ▴ 110
0
votes
0
replies
575
views
Reteroviruses in shotgun metgaenome data
genomics Metagenomics Microbial Viruses RNA-Viruses
2.4 years ago by serene.s • 0
0
votes
0
replies
760
views
News: Course - RNAseq data analysis with R/Bioconductor
R Tidyverse RNA-seq Bioconductor
updated 2.2 years ago by 45k • written 2.4 years ago by ★ 2.6k
0
votes
2
replies
1.4k
views
Somatic variant calling mutect2 ctDNA liquid biopsy
ctDNA gatk tumor Mutect2 SNP
2.4 years ago by bt_cepo ▴ 40
1
vote
1
reply
1.7k
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq short-read long-read
updated 18 months ago by 45k • written 2.4 years ago by ▴ 60
0
votes
0
replies
931
views
Questions about using Jellyfish and genomescope with paired end reads?
jellyfish genomescope
2.4 years ago by asilidae • 0
1
vote
2
replies
1.7k
views
BBmap params for accurate MAG relative abundance estimation?
abundance BBmap alignment metagenomics
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
2
votes
1
reply
932
views
Racon empty output (non-memory issue)
racon
2.4 years ago by lajordac ▴ 20
0
votes
1
reply
1.4k
views
Tool: web app for user-friendly analysis of 16S rRNA gene meta-barcoding NGS data - bacterial microbiome
qiime2 16s microbiome ngs
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
1
vote
2
replies
980
views
How do you select DEGs for further validation?
DGE-analysis DEG
2.4 years ago by marina.wakid ▴ 10
0
votes
2
replies
1.4k
views
Spatial transcriptome analysis
single_cell transcriptome Seurat spatial_transcriptome RNA-seq
2.4 years ago by siu ▴ 160
0
votes
0
replies
663
views
How do I annotate with the Clingen Canonical Allele Identifiers?
allele vcf clingen
2.4 years ago by Jeremy Leipzig 23k
0
votes
6
replies
2.4k
views
samtools and Rsamtools in r
samtools
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 80
1
vote
9
replies
1.8k
views
gene annotation
gtf gene-annotation
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
0
replies
678
views
News: Course - Multiplex imagine analysis/ Spatial Omics
Multiplex-Image-Analysis Spatial-Omics
updated 2.4 years ago by 45k • written 2.4 years ago by ★ 2.6k
0
votes
0
replies
558
views
VG Giraffe Mapping to a Single Connected Component
graph vg pangenome giraffe
2.4 years ago by jdru ▴ 10
3
votes
4
replies
2.4k
views
How to convert chromosome locations to gene symbols?
symbol location chromosome gene
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 20
3
votes
3
replies
1.2k
views
mRNA library preparation Adapter ligation
library mRNA
updated 2.4 years ago by ▴ 220 • written 2.4 years ago by • 0
1
vote
2
replies
1.6k
views
Read depth extraction
SNPs Genomics
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
2
votes
3
replies
1.1k
views
Samtools faidx can't be run in succession on two reference files?
Samtools
2.4 years ago by DdogBoss ▴ 30
0
votes
0
replies
667
views
PHLAT genotyping with scRNA-seq (10x)
PHLAT scRNA-seq 10x
2.4 years ago by malonzm1 ▴ 20
0
votes
0
replies
553
views
Sample based on allele frequency matching between two files
linkage
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 20
2
votes
2
replies
7.9k
views
Best tool for trimming and filtering nanopore direct RNA sequencing.
minion nanopore ont longread
2.4 years ago by kenneditodd ▴ 50
0
votes
4
replies
2.2k
views
Removing multi-variant records from vcf file
GATK vcf
updated 2.4 years ago by ▴ 400 • written 3.3 years ago by • 0
0
votes
1
reply
2.2k
views
GATK4 ASEReadCounter Function of VCF
GATK GATK4 VCF ASE ASEReadCounter
updated 2.4 years ago by ▴ 400 • written 3.3 years ago by • 0
2
votes
4
replies
1.8k
views
gosling.js and React 1.7+
react gosling
updated 2.0 years ago by 45k • written 3.1 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Repbase not installed error while running maker
repbase maker
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
2
votes
1
reply
4.3k
views
How to make a volcano plot including all features in a Seurat Object?
scRNA-seq Seurat
updated 2.4 years ago by 5.1k • written 2.4 years ago by ▴ 110
4
votes
2
replies
1.8k
views
ERROR(freebayes): Could not get first alignment from target
bam freebayes
2.4 years ago by arya.sagittarius ▴ 10
0
votes
1
reply
473
views
Normalizing before Metaphlan2
Metaphlan2
written 2.4 years ago by • 0
2
votes
4
replies
1.9k
views
Linkage Disequilibrium with Plink
Linkage-Disequilibrium Plink
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 10
4
votes
3
replies
3.7k
views
KING kinship inference error
king plink fam
updated 2.4 years ago by 11k • written 4.3 years ago by • 0
0
votes
2
replies
1.8k
views
bcftools get allele abundance
variant-calling bcftools
updated 2.4 years ago by ▴ 850 • written 2.4 years ago by • 0
1
vote
2
replies
1.3k
views
Tool: Tinybio Slackbot - a large language model slackbot for bioinformatics
qa
2.4 years ago by Sasha ▴ 850
2
votes
1
reply
706
views
P values on box plots
sequencing Statistics RNA
updated 2.4 years ago by ★ 2.1k • written 2.4 years ago by ▴ 10
0
votes
2
replies
833
views
How to find DNA sequence of a SNP without reference genome? (I have a .vcf file)
vcf SNP reference
2.4 years ago by Roland ▴ 20
3
votes
0
replies
1.3k
views
Herald: The Biostar Herald for Thursday, May 11, 2023
herald
2.4 years ago by Biostar 3.6k
121,991 results • Page 259 of 2440
Recent Votes
A: Trimmomatic Error: Unable to detect quality encoding
A: Trimmomatic Error: Unable to detect quality encoding
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: TMM-Normalization
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Answer: Doubt on docking by Mensur Dlakic ★ 30k
I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest. A general answer is that …
Answer: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The post looks much better now, so you did something. The preview here works fine. It simply can't be that the preview for your original po…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Black box software has its cons but in instances like what OP needs that may be the only viable option. Their use limits reproducibility as…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
Have you checked : https://www.pacb.com/connect/datasets/
Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
This question is about simulating reads and not read mapping.
Comment: GUI commercial software for 10x single cell gene expression analysis by yura.grabovska ▴ 830
I have fun memories of month-long discussions with Illumina support about their GenomeStudio methylation module asking them to provide info…
Comment: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by Arup Ghosh 3.4k
Try the references from the following publications. https://www.nature.com/articles/s41591-024-03150-z https://www.science.org/doi/10.112…
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
There's an easier way than manually renaming the output files (though you can do this, and it works) - you can use the `name` (aka `stageAs…
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Last Call for this event. Apply now, if you like to join.
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