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121,990 results • Page 257 of 2440
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2
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0
replies
588
views
Reference request for getting the big picture of gene taxonomy
genes textbook
2.4 years ago by garbagelister ▴ 20
0
votes
0
replies
644
views
Correct tRNA genes nomenclature in plant chloroplast genomes
chloroplast tRNA genes genome
2.4 years ago by Denis ▴ 320
0
votes
0
replies
878
views
Job: Senior Research Associate in Bioinformatics @ University of East Anglia, UK _+UPDATED DEADLINE
translation Cancer
2.2 years ago by dan.brewer ▴ 120
0
votes
0
replies
574
views
Perl debugging help - miRWoods
perl miRNA
2.4 years ago by Gill • 0
2
votes
6
replies
2.8k
views
how to make a venn plot with data frame in R
plot R Venn
2.4 years ago by sata72 • 0
4
votes
3
replies
1.3k
views
count protein-coding genes per contig
number protein-coding contig genes genome
updated 2.4 years ago by 6.2k • written 2.4 years ago by ▴ 110
2
votes
1
reply
1.2k
views
Extract transcript ID and gene ID from ITAG4.1_gene_models.gff
Genome Tomato
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
3
votes
1
reply
1.1k
views
Sewage covid sequence analysis using C-Wap
sequencing Pipeline RNA
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
1
vote
0
replies
737
views
normalize.quantiles in preprocessCore package with data containing missing values
preprocessCore missing normalize.quantiles value
2.4 years ago by tkmt ▴ 10
0
votes
3
replies
1.5k
views
Picard ribosome intervals list
Picard
2.4 years ago by mropri ▴ 170
1
vote
2
replies
1.0k
views
What is the command line to map XLOC_ids from cufflinks with rice LOC_ids from msu
mapping
2.4 years ago by isha.lily20 ▴ 10
0
votes
0
replies
998
views
Significance of "orientation" flag in FilterMutectCalls output
filtermutectcalls gatk VCF mutect2 SNP
2.4 years ago by bt_cepo ▴ 40
1
vote
2
replies
2.5k
views
Help with ERROR: Paired-end reads were detected in single-end read library
featureCounts
2.4 years ago by Chris ▴ 360
3
votes
4
replies
1.7k
views
Fast BAM header editing
bam
updated 2.4 years ago by ★ 4.3k • written 2.4 years ago by 36k
7
votes
6
replies
2.5k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 380
5
votes
2
replies
1.4k
views
I need to define a ground truth/correct answer set of GO terms for proteins
SwissProt GO-term GOA
updated 2.4 years ago by ▴ 470 • written 2.4 years ago by • 0
0
votes
0
replies
599
views
Comparison between z-scores of protein and mRNA levels
expression Statistics
2.4 years ago by Camilo Andres ▴ 40
1
vote
2
replies
1.1k
views
BLAST: Cobmine nr/nt database with a fasta file
blast blast_aliastool
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 10
2
votes
1
reply
692
views
emptyDrops generates different results
DropletUtils emptyDrops scRNA-seq
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 50
1
vote
3
replies
2.1k
views
Cibersort phenotpe file to create signature matrix
deconvolution cibersort phenotype
updated 2.4 years ago by ★ 1.9k • written 2.7 years ago by • 0
9
votes
15
replies
4.0k
views
How to Diagnose Fragile X from Whole Genome Sequencing
FMR1 FragileX
updated 2.4 years ago by ★ 2.5k • written 2.8 years ago by ▴ 10
1
vote
1
reply
904
views
DESeq2 with multiple factors
DESeq2
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 20
2
votes
2
replies
865
views
DESeq factor order
DESeq2
2.4 years ago by Chris ▴ 10
3
votes
9
replies
2.3k
views
Get protein information from ensemblbacteria using interpro
ensembl
updated 2.3 years ago by ▴ 10 • written 2.4 years ago by • 0
2
votes
1
reply
968
views
scRNAseq (bioconductor) data to seurat object
bioconductor seurat scRNAseq
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 20
1
vote
2
replies
892
views
StringTie across datasets
novel transcripts stringtie rna-seq
2.4 years ago by Prangan ▴ 20
1
vote
3
replies
1.6k
views
Endless Updating service celery-beat message with galaxy
galaxy
updated 2.4 years ago by 103k • written 2.4 years ago by ▴ 40
1
vote
2
replies
1.8k
views
fastq-dump - connection failed
fastq-dump sratoolkit
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 20
2
votes
4
replies
3.8k
views
best annotation approach for peaks
chipseeker R chippeakanno
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 50
0
votes
9
replies
2.6k
views
Intersecting transcriptome bam file with GTF file
findoverlaps bedtools transcriptome
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 80
2
votes
3
replies
1.8k
views
ATAC peak-calling: same peak ID across multiple experimental conditions?
Genrich ATAC
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by • 0
3
votes
5
replies
4.8k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
Differential-Expression DESeq2
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 10
4
votes
3
replies
2.9k
views
Encode project signal p-value
ChiP-Seq p-value Encode signal
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 730
2
votes
2
replies
1.4k
views
How to obtain low mappability regions from UCSC for deepTools computeGCBias?
deepTools
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 180
55
votes
6
replies
21k
views
Decoy In Reference Assembly
1000genomes
updated 2.4 years ago by • 0 • written 12.4 years ago by ▴ 440
3
votes
9
replies
1.9k
views
Estimate sizes of repeats in a especific Gene
CGG Fragile-X
2.4 years ago by Rafael ▴ 10
0
votes
1
reply
861
views
How to download data for a specific time period in GDC portal?
GDC RNA-seq portal TCGA
updated 2.4 years ago by ★ 1.3k • written 2.4 years ago by ▴ 40
0
votes
0
replies
630
views
selection of Gene Ontology terms manually
RNAseq Gene-ontology GOanalysis Clusterprofiler
2.4 years ago by harish ▴ 10
4
votes
4
replies
4.5k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 2.4 years ago by 45k • written 4.6 years ago by • 0
0
votes
0
replies
683
views
News: New version of ElasticBLAST (1.1.0) available from NCBI
ElasticBLAST BLAST. NCBI
2.4 years ago by PeterC_NCBI ▴ 520
0
votes
1
reply
639
views
Best tool for cross plate contamination removal
WTA Microbe Sequencing Assembly
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 30
1
vote
2
replies
1.4k
views
Can I use umi_tools to discard cell barcodes and extract the UMI while keeping the UMI in the read?
umitools umi_tools
updated 2.4 years ago by 22k • written 2.4 years ago by ▴ 10
4
votes
7
replies
1.6k
views
How to better distribute my replicates between two batches of bulk RNAseq?
replicates RNAseq batch-effect
2.4 years ago by Victor • 0
0
votes
0
replies
418
views
Analyzing aCGH dataset using R Programming
aCGH
2.4 years ago by Kent ▴ 30
0
votes
4
replies
1.4k
views
how to perform phylogeny to know the evolution of strains
raxml fasta
2.4 years ago by Neel ▴ 20
0
votes
0
replies
565
views
Orientation bias in variants called by mutect2
ctDNA gatk tumor Mutect2 SNP
2.4 years ago by bt_cepo ▴ 40
0
votes
0
replies
653
views
News: Course - Introduction to CRISPR for Ecology and Evolution Studies
Genomics CRISPR
2.4 years ago by Physalia-courses ★ 2.6k
3
votes
5
replies
3.9k
views
How can I update fastq-dump to 3.0.0?
fastq-dump
updated 8 weeks ago by • 0 • written 2.4 years ago by ▴ 20
0
votes
0
replies
537
views
How to align Illumina FASTQ isolates to a conserved gene for phylogenetic analysis
fastq align illumina phylogenetic
2.4 years ago by doggie • 0
0
votes
0
replies
496
views
How to load inidividual ADT and RNA data to the same AnnData structure
python CITE-seq Scanpy
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
121,990 results • Page 257 of 2440
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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
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
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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…
Answer: 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…
Answer: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 i by ecSeq Bioinformatics ▴ 20
Last Call for this event. Apply now, if you like to join.
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
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…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
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…
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