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0 votes
0 replies
560 views
Automatically annotate gene loci
reference-genome scrna-seq gene-annotation
updated by Ram 4.5K • | written by rtrende 8
0 votes
4 replies
1.9K views
One SRR (one fastq) file for pair-end layout
srr paired-end sra
written by Vojtěch 1
2 votes
6 replies
3.7K views
0 Features for COVID-19 ExpressionSet through GEOQuery
rna-seq r geoquery
updated by Sean Davis 2.7K • | written by arjuncsubra 2
2 votes
5 replies
2.4K views
Tool: ggalign: alternative to ComplexHeatmap, a ggplot2 extension for complex heatmap and marginal plots.
ggplot2 heatmap
written by Yun 9
0 votes
1 reply
768 views
Genes of Interest in a Multi-Tissue Analysis
vst dge deseq2
updated by allingt 4 • | written by Gabriel 0
0 votes
1 reply
1.0K views
Generate PSSM using HMMER
hmmer
updated by Mensur Dlakic 3.0K • | written by jet 0
0 votes
2 replies
1.3K views
Inlfated QQ plot GWAS
gwas
updated by LauferVA 497 • | written by Pedro 0
0 votes
10 replies
9.5K views
vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
vcftools vcf
updated by Ram 4.5K • | written by mayara.salvian 1
0 votes
18 replies
3.8K views
Submitting a job in parallel on slurm
bam slurm shell parallel
updated by rfran010 174 • | written by Arthur 1
0 votes
1 reply
711 views
WGS variant filtering for exome
wes snp strelka freebayes wgs
updated by Pierre Lindenbaum 17K • | written by isMM 0
0 votes
3 replies
1.0K views
Change of cell proportions or differential expression?
deconvolution differential-expression
written by Aspire 43
0 votes
7 replies
2.5K views
I encountered a problem while using Mageck to analysis CRISPR screen data
mageck crispr-screen
updated by GenoMax 16K • | written by Pallondyle 0
0 votes
9 replies
2.8K views
How do I find allele frequencies from GATK output?
allele-frequency gatk muller-plot
updated by 2nelly 35 • | written by mgranada3 6
1 vote
2 replies
1.5K views
What are the WES-specific settings when running GATK's variant recalibration step?
wes gatk recalibration exome
updated by GenoMax 16K • | written by Joel Wallenius 22
0 votes
3 replies
7.1K views
Remove column from Seurat metadata
single-cell transcriptomics cell-type-annotation rnaseq
updated by ev97 4 • | written by gorizwango 3
0 votes
3 replies
1.1K views
Difference in depth of coverage between SNIPPY and in-house script
ngs
updated by GenoMax 16K • | written by Sudheer Gupta 4
1 vote
0 replies
731 views
how to perform QTL analysis and how to integrate multi-omit datasets
r statistics genetics
written by Bioinfonext 48
0 votes
1 reply
1.8K views
How to annoate the probe id to genes in Affymetrix Human Gene 2.0 ST Array [transcript (gene) version ?
biomart geo microarray annotation
updated by ultraanfibio 4 • | written by DareDevil 448
1 vote
4 replies
2.9K views
GSEA vs GO-enrichemnt analysis
rna-seq
written by Pegasus 13
0 votes
1 reply
801 views
How To Get Millions of Sequences from Genomic Regions Efficiently
python pandas genome
updated by Ram 4.5K • | written by Yacob 0
1 vote
0 replies
599 views
dbNSFP in-silico predictor results counts not-equal to number to alternatives in vcf file
vcf
written by Lukas 13
0 votes
5 replies
2.6K views
DEGs vs WGCNA: What am I really looking at?
deseq2 rna-seq deg wgcna
written by christiantd 0
0 votes
1 reply
774 views
Feature selection for normalized RNA-seq data
feature-selection rna-seq
updated by pinheirofabiano 14 • | written by leila 0
0 votes
3 replies
1.4K views
How to convert h5ad object to rds object without raw counts?
h5ad
updated by yura.grabovska 94 • | written by hejenny792 0
1 vote
2 replies
2.8K views
Subsetting cells from a previously integrated Seurat dataset (scRNA-seq)
subclustering scrna-seq seurat
updated by heidenreich.ac 0 • | written by Song 1
0 votes
3 replies
1.3K views
Check if a BAM file is corrupt in Java
bam java
updated by Pierre Lindenbaum 17K • | written by Bertalan_Takacs 14
0 votes
4 replies
2.7K views
Cannot download BUSCO datasets
busco
written by JenI 0
0 votes
1 reply
1.5K views
Unable to Upload a .txt file into GSEA
txt dataset gsea expression
updated by GenoMax 16K • | written by BUB1 0
0 votes
0 replies
682 views
How to plot phylogenetic tree(dendrogram) of mitochondria haplogroups?
phylogenetic haplogroups mtdna dendrogram
written by Karibu 0
0 votes
6 replies
1.4K views
RNA seq mapping
rna-seq
updated by Ram 4.5K • | written by mohamadhosein.shams1381 0
2 votes
14 replies
4.0K views
Proper reanotation of genepanel with snpEff and dbNSFP
vcf
written by Lukas 13
0 votes
3 replies
2.1K views
Header too long for bam format
samtools alignments
updated by Ram 4.5K • | written by selplat21 2
0 votes
2 replies
970 views
bam file: unmapped but matching reads (samtools view -f 4)
samtools bam
updated by Pierre Lindenbaum 17K • | written by Tommy 0
0 votes
2 replies
1.3K views
Converting OMA IDs to Ensembl gene names
orthologs oma ensembl
updated by Ram 4.5K • | written by Eric 0
1 vote
1 reply
948 views
Guidance on Reference-Based Assembly and Variant Analysis of Exome Sequencing Data
samtools bcftools genome wgs bwa-mem
updated by aw7 40 • | written by Rohan 4
0 votes
1 reply
782 views
Linear regression models on non-linear dataset
correlation regression
updated by dthorbur 350 • | written by mrashad 9
6 votes
0 replies
1.9K views
Tutorial: 6 tips to stay up to date for bioinformatics
bioinformatics computational-biology
updated by Ram 4.5K • | written by Ming Tommy Tang 469
0 votes
4 replies
1.6K views
Nanopore cDNA sequencing - primary and complementary strand in one read
cdna nanopore
updated by GenoMax 16K • | written by ovovo 0
0 votes
3 replies
1.3K views
Can any one help me in intersect and merge in my correlation plot ?
corrplot rscript correlation
written by isha.lily20 1
1 vote
2 replies
1.4K views
Tools to call structural variants in haploid yeast from WGS data
structural-variants wgs yeast variant-calling
updated by clealk 8 • | written by Tasneem Fetian 2
0 votes
4 replies
1.3K views
RNA seq data for normal samples
rna-seq
updated by Raag 2 • | written by maryak 2
0 votes
5 replies
1.5K views
STAR cannot read fastq files
mapping star
updated by biofalconch 132 • | written by spela.j 1
0 votes
3 replies
1.4K views
Discrepancy between VCF and BAM file.
ngs bwa haplotypecaller gatk
updated by Ram 4.5K • | written by franklin 0
0 votes
0 replies
430 views
deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling
decorda
updated by Ram 4.5K • | written by Ana 0
0 votes
1 reply
809 views
Gene Enrichment Analysis
gene-ontology enrichment go
updated by Ram 4.5K • | written by BioGeek 17
1 vote
1 reply
3.0K views
Lastz multi thread options
lastz alignment
updated by Ram 4.5K • | written by BioGeek 17
2 votes
14 replies
23K views
Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed Genes) to confirm results together- is it a good idea?
rna-seq r sequencing
updated by arnaud_p 0 • | written by chokevin8 3
0 votes
1 reply
1.4K views
extracting cell specific reads from cellranger BAM output file
bam cellranger seurat
updated by Ram 4.5K • | written by singcell 1
0 votes
1 reply
1.0K views
PCA Genotyping rate 1000genome and own data
quality genotypingrate pca plink genomics
updated by LChart 518 • | written by curious_butterfly 0
0 votes
2 replies
1.0K views
eQTL analysis for the same population in different status
eqtl
written by jlshi.nudt 24
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