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15
replies
8.2k
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How to Extract Specific Region on Bam file
Nanopore HG38 Rna-Seq Genome
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 40
12
votes
2
replies
5.4k
views
Add NES value to GSEA plot
R enrichplot clusterprofiler GSEA
updated 4.3 years ago by ★ 1.3k • written 4.4 years ago by ▴ 50
2
votes
4
replies
1.7k
views
Viral metagenomics of RNA virus on transcriptomics data workflow
Viral metagenomics workflow
4.3 years ago by bioAddict • 0
1
vote
0
replies
631
views
Tripal insert menu items
tripal
4.3 years ago by felipead66 ▴ 120
11
votes
10
replies
9.1k
views
What exactly should and shouldn't go in Combat's model matrix?
batch effects expression gene combat
updated 4.3 years ago by ★ 3.1k • written 4.4 years ago by ▴ 390
2
votes
4
replies
1.5k
views
Needs recommendation - Variant Call from RNA seq data of tumor-normal pairs.
variant call tumor-normal RNA-seq
4.3 years ago by field654 ▴ 30
2
votes
3
replies
1.1k
views
export alignment from BAM file
bam samtools
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
765
views
Select random sequences matched by distance to TSS and width
tss sequences random
4.3 years ago by carinapaola20 • 0
2
votes
1
reply
1.2k
views
Gffread extracts the wrong nucleotides from genome
transcriptomics harvesting genome gff3 gffread sequence
4.3 years ago by stephanbitterwolf ▴ 20
11
votes
8
replies
3.5k
views
PHRED scores and sequence errors
sequencing-errors probability PHRED
updated 2.4 years ago by 45k • written 4.3 years ago by ★ 2.9k
0
votes
1
reply
2.6k
views
Filter GQ , DP and Allele Balance in VCF
bcftools balance allele alllele vcf
updated 4.3 years ago by ▴ 480 • written 4.3 years ago by • 0
1
vote
6
replies
2.2k
views
HeatMap
dittoseq heatmap
4.3 years ago by barix ▴ 20
3
votes
2
replies
2.0k
views
Binding matrix created by DiffBind
DiffBind atac-seq dba
updated 2.3 years ago by 45k • written 4.3 years ago by ▴ 20
3
votes
8
replies
2.2k
views
Edit Headers of Fasta file
header fasta
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
1
reply
686
views
Gene network
Gene network
updated 4.3 years ago by • 0 • written 4.3 years ago by ▴ 10
0
votes
7
replies
2.7k
views
Trimming SOLiD adapters
SOLiD adapters Trimming
updated 4.3 years ago by 35k • written 4.3 years ago by • 0
2
votes
2
replies
1.2k
views
Available annotation file for the PacBio Iso-seq data
sequencing
updated 4.3 years ago by 154k • written 5.7 years ago by ▴ 280
1
vote
0
replies
1.4k
views
Job: Coral Bioinformatics Postdoc at Hawaii Institute of Marine Biology
Climate_Change Coral Selective_Breeding
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
12
votes
3
replies
3.8k
views
Choosing the right pathways among gene set enrichment analysis results
GSEA
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 30
0
votes
0
replies
1.3k
views
Issues with BRAKER2 (v.2.1.6)--not producing "genemark_hintsfile.gff.prot.tmp"
annotation
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
1
vote
10
replies
3.3k
views
Problem with this error: EXITING because of INPUT ERROR: the file format of the genomeFastaFile
RNA-seq alignment STAR
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
1
vote
8
replies
2.7k
views
IPA Core Analysis
RNA-Seq
4.3 years ago by Francois Piumi ▴ 70
15
votes
8
replies
8.9k
views
6 follow
GATK BaseRecalibrator known-sites vcf file
gnomad baserecalibrator gatk
updated 2.2 years ago by ▴ 110 • written 4.3 years ago by ▴ 60
6
votes
8
replies
9.7k
views
How to create a signature matrix based on a given single cell RNA-seq data
Cibersort DWLS MAST signature-matrix single-cell-RNAseq
updated 4.3 years ago by ★ 19k • written 4.3 years ago by ▴ 20
0
votes
0
replies
812
views
News: Online training - Phylogenomics
Phylogenomics
4.3 years ago by Physalia-courses ★ 2.6k
3
votes
1
reply
2.8k
views
Illumina paired end fastq sequence identifiers and index primers
fastq primers identifiers Illumina
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 10
4
votes
13
replies
3.2k
views
bcftools mpileup sample labels, seg fault
bcftools mpileup
4.3 years ago by Gregor Rot ▴ 550
0
votes
0
replies
782
views
Calculating Distance Matrix
Absence Matrix Presence Gene Distance
updated 4.3 years ago by 35k • written 4.3 years ago by • 0
0
votes
0
replies
971
views
Appropriate tool to deconvolute complex Sanger chromatograms in order to retrieve specific DNA barcodes
sequencing NGS sanger deconvolution clontracer clonality
4.3 years ago by l.beumers • 0
7
votes
5
replies
2.5k
views
Is there a way to extract alignment score from STAR aligner bam files?
rnaseq
4.3 years ago by simplitia ▴ 130
8
votes
3
replies
1.7k
views
3D protein structure prediction
3D-protein-structure
updated 4.3 years ago by ▴ 390 • written 4.3 years ago by ▴ 20
9
votes
4
replies
1.7k
views
Locating a single cell data set
scRNA-seq
updated 4.3 years ago by 7.6k • written 4.3 years ago by ★ 4.4k
0
votes
0
replies
1.4k
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
4.3 years ago by Erin Haskell ▴ 470
0
votes
0
replies
1.1k
views
Programmatically adding hydrogen and remove water to multiple PDB files
docking pdb python structure
4.3 years ago by gundalav ▴ 380
0
votes
0
replies
731
views
PC loading plot
SNP PCA plink
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 10
1
vote
0
replies
584
views
DESeq2: One or more designs for contrasts of interest
DESeq2 design contrasts
4.3 years ago by Mirin1357 ▴ 10
1
vote
0
replies
1.8k
views
Tutorial: Slurm and parallelization
slurm
4.3 years ago by Juke34 9.3k
4
votes
7
replies
2.4k
views
Mask a SNP before imputation
genotype bcftools impute2 mask VCF
4.1 years ago by raalsuwaidi ▴ 110
1
vote
4
replies
3.5k
views
Problem with Deseq2
galaxy Deseq2 sequencing RNA-seq
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 60
2
votes
7
replies
4.2k
views
Differential Gene expression between low survival and high survival samples from RNAseq
rna-seq R DEG Survival
updated 4.3 years ago by • 0 • written 7.5 years ago by ▴ 70
1
vote
4
replies
3.2k
views
Install R package fgsea: Error in download.file
bioconductor R package fgsea
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 250
0
votes
1
reply
779
views
Use part of the name of the input file in the Snakemake
snakemake
updated 4.3 years ago by 21k • written 4.3 years ago by ▴ 100
0
votes
0
replies
865
views
Job: Postgraduate Scholarship in Bioinformatics and Liver Cancer Genomics
NGS Cancer_genomics scRNA-seq Single-cell_sequencing Liquid_biopsy
4.3 years ago by waihungh ▴ 20
0
votes
1
reply
698
views
Chimpanzee genome for APE113 and APE114
Chimpanzee APE113
updated 4.3 years ago by 16k • written 4.3 years ago by • 0
0
votes
3
replies
1.7k
views
Using Linear Regression on Genotype and Expression data
Regression SNP Machine Learning Genotype
updated 4.3 years ago by ▴ 110 • written 4.3 years ago by ▴ 30
2
votes
3
replies
1.6k
views
what is the corelation between Elastic net method and GAIA method?
genes prediction
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 260
1
vote
2
replies
1.9k
views
Getting peak (bed narrowPeak) from signals (Wig)
data ChIP-seq analysis
4.3 years ago by arsala521 ▴ 60
0
votes
1
reply
985
views
Supernova 10X Genomics - estimation of gap length
gap_length_estimation 10X_Genomics genome_assembly Supernova_assembler
4.3 years ago by MH85 ▴ 20
0
votes
0
replies
782
views
Error: SLAC of HyPhy tool Galaxy.org
hyphy galaxy slac
4.3 years ago by frk • 0
0
votes
0
replies
762
views
Minimum size of input genes list and number of samples for fgsea
gsea fgsea
4.3 years ago by confused but trying • 0
121,989 results • Page 631 of 2440
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Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Quantification using salmon in alignment-based mode after minimap2 run
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?
A: Bioinformatic Cartoon
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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…
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…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
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…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
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…
Answer: meta data analysis for clustering by Meisam ▴ 250
I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
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