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673
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Correct way to write the names in the "product" field of a GTF file
gtf rnaseq annotation
4.3 years ago by arturo.marin ▴ 20
2
votes
2
replies
1.4k
views
How to convert ONT longread or illumina fastq to fasta file
denovo assembly genome
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 10
1
vote
1
reply
1.5k
views
BGENIE vs REGENIE
bgenie regenie
updated 4.3 years ago by ▴ 40 • written 4.5 years ago by ▴ 20
2
votes
3
replies
2.0k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta Nanopore long-read fastq
updated 18 months ago by 45k • written 4.3 years ago by ▴ 10
0
votes
0
replies
603
views
De novo assembly Sacffolding tool for long reads
genome scaffold
4.3 years ago by K ▴ 10
2
votes
2
replies
1.1k
views
How do I call compound hetrozygosity from multiple trios cohort?
ped gatk trio heterozygosity compound vcf
4.3 years ago by DareDevil ★ 4.4k
5
votes
6
replies
2.7k
views
How to check which genes affect a continuous phenotype
multiple-comparisons multiple-regression microarrays regression
4.0 years ago by Aspire ▴ 390
1
vote
7
replies
2.5k
views
Statistics of amino acid usage of multiple aligned sequences?
alignment
updated 4.3 years ago by 22k • written 6.6 years ago by ▴ 110
4
votes
2
replies
1.7k
views
Validate input file as BED file
R BED
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 40
0
votes
2
replies
901
views
Genotype
genetic
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
2
replies
3.5k
views
problem for installing packages
ReactomePA
4.3 years ago by fahim ▴ 20
3
votes
4
replies
5.4k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 17 months ago by 45k • written 4.3 years ago by ▴ 80
0
votes
0
replies
667
views
Counting number of NSMs from WES variants
variants VCF WES SNPEFF
4.3 years ago by tomer9w • 0
2
votes
2
replies
1.5k
views
Get read id's from .sam file
sam
updated 4.3 years ago by 166k • written 4.3 years ago by ▴ 80
1
vote
0
replies
674
views
functional annotation and gene quantification
functional shotgun annotation
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
0
votes
0
replies
565
views
SNP tissue expression
R GTEx
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 10
3
votes
1
reply
1.2k
views
What is the fastest way to create an online server that allows searching through a table
database searchable online query
updated 4.3 years ago by ★ 2.2k • written 4.3 years ago by ▴ 100
0
votes
0
replies
832
views
How to determine protein subsites?
Protein 3D Pymol
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
0
votes
1
reply
858
views
How to interpret terms with “positive” and “negative” specifiers
gene GO term ontology
4.3 years ago by chriselhadi • 0
2
votes
1
reply
1.0k
views
Error: unexpected symbol using BiomaRt in R
ensembl r biomart biomaRt R
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
4
votes
1
reply
2.8k
views
How to tell if enrichment is good or bad from GSEA plot
genes gsea enrichment
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 380
3
votes
2
replies
1.0k
views
whole genome analyses
python
updated 4.3 years ago by • 0 • written 4.3 years ago by ▴ 20
3
votes
5
replies
3.1k
views
generate FASTA/MSA from VCF file
VCF MSA FASTA
updated 3.7 years ago by ▴ 40 • written 4.3 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Primer matching with sequence using biopython
primers Biopython alignment
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by • 0
0
votes
4
replies
2.5k
views
Can't index .bed file with tabix
bed tabix leafcutter
updated 4.3 years ago by ★ 4.3k • written 4.3 years ago by • 0
1
vote
2
replies
1.3k
views
Fasta file for Whole exome sequencing analysis
WES Gencode
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.3k
views
Snakefile - problem with too many outputs
snakemake snakefile
updated 4.3 years ago by ★ 1.5k • written 4.3 years ago by ▴ 30
0
votes
0
replies
871
views
LOESS Normalization Explanation
proteomics pre-processing InfernoRDN normalization
4.3 years ago by gt ▴ 30
0
votes
5
replies
1.8k
views
about bowtie parameter --fr and --rf
ATAC reads paired bowtie2
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Combining NES and FDR q-values over gene set clusters (Enrichmentmap) in GSEA
GSEA
4.3 years ago by lsy9 ▴ 20
2
votes
3
replies
1.4k
views
Get upstream and downstream exon's starting site and ending site of an retained introns
RNAseq
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 130
3
votes
3
replies
4.1k
views
GCTA make GRM error contains illegal chr number
plink GCTA
4.3 years ago by Star:) ▴ 50
0
votes
0
replies
456
views
Combining 2 sets of samples.
Gwas
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
5
replies
1.6k
views
FeatureCounts Number of Reads
RnaSeq FeatureCounts
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 40
7
votes
3
replies
2.0k
views
high duplication events in shotgun metagenomics
MAG metagenomics duplication
4.3 years ago by alexis ▴ 30
3
votes
7
replies
5.2k
views
Plink 1.9 "File read failure" error when merging with --bmerge
plink gwas error
updated 4.3 years ago by ▴ 40 • written 6.7 years ago by ▴ 20
0
votes
1
reply
732
views
Dual RNA-seq differential gene expression analysis
deseq2 rnaseq dual
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
4
replies
1.7k
views
Compare gene coverage across group o samples
gene coverage
4.3 years ago by roalva1 ▴ 100
5
votes
13
replies
3.6k
views
Bowtie2 problem when use aligned or unaligned output file for re-alignment
bowtie2
4.3 years ago by daewowo ▴ 80
0
votes
0
replies
759
views
retrieve all significant motifs from meme suite programs
meme
4.3 years ago by boczniak767 ▴ 880
0
votes
2
replies
1.1k
views
How can each file be commanded separately with multiple files in R??
R
updated 2.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
1
reply
2.1k
views
What format should a dataframe be in to use the AddMetaData function in Seurat?
seurat R RNA-Seq rna-seq scRNA-seq
4.3 years ago by Pratik ★ 1.1k
9
votes
5
replies
16k
views
How to read a dataframe into Seurat for AddMetaData properly?
seurat rna-seq RNA-Seq R
4.3 years ago by Pratik ★ 1.1k
0
votes
0
replies
1.4k
views
MGLTOOLS
Docking Autodock Macbook MGLTools
4.3 years ago by Farnoosh • 0
0
votes
1
reply
998
views
Does anyone know what BLASTN exact match of 11 means in layman terms?
Blastn Blast
updated 4.3 years ago by 11k • written 4.3 years ago by • 0
0
votes
0
replies
1.3k
views
How to perform Synteny analysis for a single gene?
alignment SNP genome gene R
4.3 years ago by anikcropscience ▴ 270
9
votes
2
replies
9.0k
views
Run STAR on .fastq files I1, R1 and R2
RNA-seq alignment STAR
4.3 years ago by PianoEntropy ▴ 70
8
votes
7
replies
1.8k
views
Co-occurrence of proteins of two families
proteins BLAST Co-occurrence
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by ▴ 50
2
votes
2
replies
1.2k
views
help for genNullSeqs()
genNullSeqs
4.3 years ago by koyee_d ▴ 20
0
votes
0
replies
600
views
JContextExplorer
software JContextExplorer
4.3 years ago by K.Gee ▴ 40
121,990 results • Page 630 of 2440
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Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
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Answer: Quantification using salmon in alignment-based mode after minimap2 run
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Corresponding BAM files
Answer: Tools To Calculate Average Coverage For A Bam File?
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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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The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
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I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
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hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
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Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
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I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
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