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121,983 results • Page 250 of 2440
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5
votes
7
replies
4.3k
views
How to calculate TPM from featureCounts output
rna-seq TPM featurecounts
updated 2.3 years ago by ★ 1.7k • written 2.3 years ago by • 0
3
votes
11
replies
6.6k
views
7 follow
How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?
10xgenomics RNAseq scRNA CB
updated 14 months ago by 154k • written 3.2 years ago by ▴ 20
0
votes
0
replies
504
views
Prediction of altrered metabolites from altered gene expression
Gene Metabolites
2.3 years ago by english.server ▴ 300
2
votes
3
replies
1.5k
views
CNNScoreVariants Error
CNNscore
updated 2.3 years ago by 166k • written 2.3 years ago by ▴ 30
3
votes
1
reply
711
views
Finding Enhancers using Genomation library
Genomation
2.3 years ago by Pankaj • 0
0
votes
5
replies
3.2k
views
convert data frame with character column to data frame with integer column
r
updated 2.3 years ago by ★ 2.1k • written 2.4 years ago by • 0
0
votes
0
replies
466
views
Pore-C-Snakemake output files
contacts
updated 2.3 years ago by ▴ 50 • written 2.4 years ago by • 0
6
votes
3
replies
1.4k
views
Why is coordinate sort required before findng read depths?
wgs sambamba
updated 2.3 years ago by ▴ 50 • written 2.4 years ago by ▴ 40
4
votes
2
replies
1.5k
views
how to sort unique seq from fasta files
fasta
updated 2.3 years ago by 8.7k • written 2.3 years ago by ▴ 10
2
votes
2
replies
969
views
I need help with a blast command, please help
linux blast
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
1
vote
1
reply
1.2k
views
Is there a way to add a transcript to EnsDb.Hsapiens.v86?
ensembldb GenomicFeatures R Bioconducter EnsDb.Hsapiens.v86
2.3 years ago by Daniel ▴ 40
2
votes
2
replies
1.5k
views
How to make the profile line of `deepTools::plotHeatmap` more smooth?
plotHeatmap deepTools
2.3 years ago by Dan ▴ 180
0
votes
3
replies
1.1k
views
Convert Bam file to Fastq
Fastq Bam
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
0
replies
1.4k
views
Job: Data Engineer / Bioinformatician- AZ-Crick-Imperial College: Molecular Glue Discovery Partnership
data-engineering drug-discovery data-science
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 230
0
votes
6
replies
1.8k
views
variant allelic fraction
vep
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
2
replies
900
views
WGCNA Trait File Issues
correlation Deseq2 Gene WGCNA
updated 2.3 years ago by 5.1k • written 2.3 years ago by • 0
0
votes
1
reply
896
views
Pairwise Alignment
Pairwise-Alignment
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
3
votes
6
replies
9.2k
views
h5ad cellxgene to R
single-cell h5 cellxgene anndata R
2.3 years ago by firestar ★ 1.7k
4
votes
6
replies
2.2k
views
calculate p value and associated z score for snp-gene pair
snp association gene pvalue
2.3 years ago by rheab1230 ▴ 150
1
vote
3
replies
1.3k
views
What is the benefit of knowing the source of contamination when we have RNAseq data with less than 70% mapping?
alignment mapping STAR contamination RNAseq
2.3 years ago by Sib ▴ 80
0
votes
0
replies
613
views
How to perform a phylogenetic analysis from a vcf file
variants haplotyping phylogeny vcf
2.3 years ago by rj.rezwan ▴ 20
0
votes
3
replies
1.4k
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA database
updated 2.3 years ago by ★ 1.3k • written 2.3 years ago by ▴ 60
2
votes
2
replies
1.7k
views
Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads that have MT in RNEXT field
samtools ATAC-Seq mitochondrial-reads RNEXT
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
1
vote
5
replies
1.8k
views
Is a human genome file with reference as NCBI37 the same as hg19?
vcf hg19 genome reference-genome
updated 2.3 years ago by 154k • written 2.3 years ago by ▴ 10
7
votes
4
replies
1.9k
views
Forum: [Meta] Use of AI
AI Artificial-Intelligence meta ChatGPT
updated 2.3 years ago by 45k • written 2.3 years ago by 4.8k
0
votes
0
replies
811
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram HeatmapAnnotations R Heatmap ComplexHeatmap
2.3 years ago by Manuel ▴ 10
5
votes
6
replies
1.9k
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq RSubreads
2.3 years ago by Yeeshouw ▴ 10
1
vote
2
replies
971
views
Random dataset and DESeq2
DESeq2
updated 2.3 years ago by 4.8k • written 2.3 years ago by • 0
1
vote
1
reply
920
views
Network cross-validation
wgcna RNASeq Network CV
updated 2.3 years ago by 5.1k • written 2.3 years ago by ▴ 550
2
votes
3
replies
1.8k
views
Differential protein expression analysis
R proteomic statistics
updated 2.3 years ago by ★ 7.7k • written 2.3 years ago by ▴ 80
0
votes
3
replies
1.4k
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2 align_stats trinity
2.3 years ago by eimanpharmacist ▴ 20
1
vote
2
replies
1.1k
views
I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
WGS
updated 2.3 years ago by 45k • written 2.3 years ago by • 0
0
votes
4
replies
1.7k
views
What are recommended parameters for the local protein alignment ?
protein alignment
2.3 years ago by Alexander ▴ 220
0
votes
0
replies
573
views
microsatellite, SSR, using Galaxy
Galaxy SSR using microsatellite
2.3 years ago by m.esmaeilpour ▴ 10
2
votes
2
replies
2.1k
views
integrate single cell RNA sequencing data
scRNAseq single-cell
updated 2.3 years ago by 3.3k • written 2.4 years ago by ▴ 120
4
votes
7
replies
2.0k
views
How to sort gff3 according to chromosome order?
gff3 sort
updated 2.4 years ago by 166k • written 2.4 years ago by • 0
2
votes
3
replies
1.6k
views
Low mapping percentage
mapping STAR RNAseq
2.3 years ago by Sib ▴ 80
0
votes
0
replies
735
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential visualization RNASeq analysis expression enrichment
2.4 years ago by Mark • 0
4
votes
3
replies
2.4k
views
What does canonical transcript mean in the context of VEP
vep
updated 2.3 years ago by 4.8k • written 2.4 years ago by ▴ 900
0
votes
0
replies
1.3k
views
Job: Postdoctoral Research Associate in bio-ontologies and machine learning (Imageomics)
Machine-Learning PostDoc Data-Science Biology Ontology
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
3
votes
4
replies
1.7k
views
bcftools "--filter-logic" flag, what + means?
bcftools vcf
updated 2.3 years ago by ▴ 540 • written 2.4 years ago by ▴ 190
0
votes
0
replies
798
views
busco id description
OrthoDB BUSCO
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
5
replies
1.7k
views
how to Construct a Newick tree file from five large fasta files
tree Newick alignment
updated 2.4 years ago by 22k • written 2.4 years ago by ▴ 20
2
votes
7
replies
2.8k
views
What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein alignment
updated 2.3 years ago by 4.8k • written 2.4 years ago by ▴ 220
0
votes
0
replies
811
views
NMDS plotting issue
NMDS metagenomic
2.4 years ago by arshad1292 ▴ 110
0
votes
2
replies
1.1k
views
featurecounts not working on mirbase annotation file
usegalaxy miRNA-seq
2.3 years ago by demoraesdiogo2017 ▴ 120
0
votes
0
replies
932
views
News: Generalized Linear Models (GLM) course in R
R GLM statistics
2.4 years ago by Physalia-courses ★ 2.6k
0
votes
0
replies
524
views
IGV insertions
insertions IGV
2.4 years ago by christoph.schubart • 0
1
vote
0
replies
659
views
Bayesian network for biological data using bnlearn
bnlearn RNA-seq bayesian-network
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
0
votes
0
replies
529
views
jellyfish options
kmer jellyfish
2.4 years ago by Tele • 0
121,983 results • Page 250 of 2440
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
Answer: Dorado in PowerShell on Windows
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: When to merge RNA-seq files with multiple sequencing lanes
Answer: When to merge RNA-seq files with multiple sequencing lanes
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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…
Answer: 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…
Answer: Analyzing CRISPR and RNAi genome wide screens by Meisam ▴ 250
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…
Comment: convert genome file to transcriptome file by Ales ▴ 50
Should be noted that the gtf/gff and genomic.fna files for HIV only contain CDS annotations of the 9 ORFs and not the full transcripts. Onl…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
just wanted to follow up that to address this specific issue we just released HIV transcriptome annotations of alternative splicing featuri…
Answer: GTF file for HIV strain pNL4-3 by Ales ▴ 50
For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the HXB2 (…
Comment: Dorado in PowerShell on Windows by sbissi102 ▴ 10
Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by DdogBoss ▴ 20
Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
Answer: GUI commercial software for 10x single cell gene expression analysis by Nicole • 0
Many researchers use the CLC Genomics Workbench and Ingenuity Pathway Analysis. CLC can be used to do secondary analysis for your dataset a…
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