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121,984 results • Page 251 of 2440
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0
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0
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529
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jellyfish options
kmer jellyfish
2.4 years ago by Tele • 0
0
votes
1
reply
1.3k
views
Diffbind not calling sites as differentially bound
DiffBind
updated 2.4 years ago by ★ 2.1k • written 3.1 years ago by • 0
1
vote
3
replies
1.0k
views
hardfilter error
bam recall
2.4 years ago by bestone ▴ 30
0
votes
0
replies
740
views
cnetplot enrichment graph to cytoscape
clusterprofiler cnetplot enrichplot
2.4 years ago by Omics data mining ▴ 260
0
votes
0
replies
549
views
How to extract the surrogate variables from DNA methlation Data
sva array limma methylation
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
1
vote
1
reply
1.6k
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap Nanopore IGV
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 50
0
votes
5
replies
3.1k
views
All combinations of two columns R
R
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
0
replies
670
views
Convert tree into bifurcation table
Tree Newick ASR Mutation
2.4 years ago by Alexandre • 0
1
vote
3
replies
1.2k
views
how to call variants in haploid genome
haploid-genome
23 months ago by itsmesmb • 0
0
votes
1
reply
1.2k
views
Processing WES VCF for case control GWAS analysis
GWAS PLINK
updated 2.4 years ago by ▴ 540 • written 2.4 years ago by • 0
4
votes
2
replies
1.6k
views
How to extract haplotype data from phased bcf files
gwas vcf bcftools wgs phasing
2.1 years ago by Lynne-95 ▴ 20
0
votes
1
reply
668
views
DE genes across multiple scRNAseq clusters-are they significantly enriched?
Single-cell
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
4
votes
6
replies
3.6k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 2.4 years ago by • 0 • written 3.2 years ago by ▴ 20
3
votes
3
replies
1.5k
views
Make a BedGraph file
BedGraph RepeatMasker BED
2.3 years ago by kirillkirilenko ▴ 40
1
vote
2
replies
1.1k
views
The famous WGS dataset, Ashkenazi Trio?
wgs dataset
updated 2.4 years ago by • 0 • written 2.4 years ago by ▴ 10
2
votes
3
replies
2.0k
views
What is the best way to clean bulk RNA-seq data?
normalization TPM r
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 200
11
votes
8
replies
2.2k
views
7 follow
BioInformatics, Software
Learning Software
updated 2.4 years ago by ★ 1.7k • written 2.4 years ago by ▴ 40
4
votes
4
replies
2.0k
views
Optimum setting for local blastp for ~10K sequences
blast blastp hpc
2.3 years ago by sodiumnitrate ▴ 20
1
vote
0
replies
607
views
Integrating mRNA and microRNA analysis results
mRNA microRNA
2.4 years ago by abba647 ▴ 10
4
votes
5
replies
1.6k
views
Does adding reads cause batch effects?
kallisto RNAseq
2.3 years ago by bioinfo ▴ 160
1
vote
2
replies
787
views
Merge different vcf files
vcf
19 months ago by caique.manochio • 0
11
votes
4
replies
3.1k
views
how to sort a fasta file
fasta
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 50
0
votes
4
replies
1.1k
views
Identification of genes involved in my pathway
KEGG keggGet
2.4 years ago by smanzano250800 • 0
5
votes
2
replies
1.7k
views
How to detect specific genes in metagenomics data
metagenomics genes
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
10
votes
14
replies
5.5k
views
ggsave() bug in ggplot2?
R ggplot2
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 20
1
vote
7
replies
1.5k
views
How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ?
SNP GATK
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 30
0
votes
8
replies
2.1k
views
The inchworm process failed. Trinity running error.
inchworm transcriptome trinity
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
1
vote
2
replies
1.3k
views
Combination of ROC CURVE
roccurve R AUC
2.3 years ago by Maria17 ▴ 40
4
votes
4
replies
2.1k
views
Understanding Used Assembly: Why aren't authors specific about patch version?
1000genomes GRCh38 gnomad assembly freeze
updated 2.2 years ago by 154k • written 2.4 years ago by ▴ 250
0
votes
1
reply
2.9k
views
what is the difference between FindVariableFeatures and FindAllMarkers?
Seurat single-cell FindVariableFeatures FindAllMarkers RNA-Seq
updated 2.4 years ago by 13k • written 2.4 years ago by ★ 1.9k
0
votes
6
replies
1.6k
views
Impute haplotypes (ImputePipelinePlugin) execution error - PHG
phg
2.3 years ago by jrodrigu • 0
1
vote
0
replies
642
views
Considering gaps in calculating conservation score from MSA
multiple alignment sequence conservation python
2.4 years ago by Jonathan Lefebre ▴ 70
8
votes
7
replies
1.7k
views
including samples for which group is unknown to help adjust for another variable
TCGA design RNA-Seq deseq2
updated 2.4 years ago by 4.8k • written 2.4 years ago by ▴ 120
0
votes
2
replies
912
views
Data is not displaying in DATABASE......error is not showing in IDE
SERVER DATABASE PHP
2.3 years ago by Souvik • 0
0
votes
3
replies
1.1k
views
DEGseq for multiple samples
DEGseq DEG
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
4
votes
2
replies
2.0k
views
How to calculate kinship matrix table from vcf file
variants haplotyping kinship heatmap
updated 2.4 years ago by 11k • written 2.4 years ago by ▴ 20
3
votes
1
reply
1.1k
views
How to convert bed file to vcf?
vcf bed
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 10
0
votes
0
replies
471
views
Metabolomics Data Annotation
annotation metabolomics camera
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 10
3
votes
4
replies
1.5k
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu hic pairtools aws
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
2
votes
2
replies
950
views
bioinformatic analysis protocol performed by CD Genomics
Genomics analysis CD Protocol
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 10
3
votes
12
replies
5.0k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 2.4 years ago by ▴ 130 • written 6.0 years ago by ▴ 10
1
vote
1
reply
1.1k
views
BAM creation - vg surject vs vg mpmap output
mpmap surject vg bam
updated 2.4 years ago by ▴ 10 • written 2.4 years ago by ▴ 130
0
votes
0
replies
604
views
RRBS fastq - biased per base sequence content
fastqc rrbs
2.4 years ago by mbk0asis ▴ 700
0
votes
0
replies
802
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates pangenome genomic
2.4 years ago by LauferVA 4.8k
0
votes
1
reply
948
views
Michigan Imputation Server - Local docker image
genotype WGS imputation
updated 2.4 years ago by 4.8k • written 2.4 years ago by • 0
0
votes
1
reply
803
views
Manhattan Plot with independent significant hits
Manhattan-plot
updated 2.4 years ago by 4.8k • written 2.4 years ago by • 0
0
votes
0
replies
512
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed ATAC-seq
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
1
vote
3
replies
903
views
To call variants can I use my aligned WGS data as a reference genome
VCF samtools reference-genome
updated 2.3 years ago by 45k • written 2.4 years ago by • 0
0
votes
1
reply
943
views
snpEff error. No CDS checked
snpEff gtf WES
updated 14 months ago by • 0 • written 2.4 years ago by ▴ 90
1
vote
2
replies
1.1k
views
how to look for interactions between different chromosomes
SNP interactions Gene HiC
2.4 years ago by rheab1230 ▴ 150
121,984 results • Page 251 of 2440
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Answer: Corresponding BAM files
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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…
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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…
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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