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1 vote
2 replies
975 views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated by GenoMax GenoMax • written by triplee0305 • triplee0305
1 vote
11 replies
2.8K views
RNASeq bulk transcriptomics analysis
rnaseq trimgalore genecounts star fastqc
written by rajdeepboral00 • rajdeepboral00
0 votes
1 reply
1.3K views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated by GenoMax GenoMax • written by QURROTU AINI • QURROTU AINI
0 votes
2 replies
1.2K views
Download GenomicSEM reference file
genomicsem
updated by 1769mkc 1769mkc • written by zhangmyharper • zhangmyharper
0 votes
11 replies
3.1K views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem bwa alignment
updated by Darked89 Darked89 • written by curious curious
0 votes
0 replies
757 views
News: UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization genomics cancer
written by Mary Goldman • Mary Goldman
0 votes
0 replies
779 views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization deseq2 host-pathogen rna-seq
written by r-ninja • r-ninja
0 votes
0 replies
625 views
Does vg stats support gaf file?
vg
written by Wang Cong • Wang Cong
0 votes
1 reply
906 views
Longest Protein per Gene from gpff file
protein gpff
updated by lieven.sterck lieven.sterck • written by reza reza
0 votes
4 replies
2.2K views
Modify read groups in BAM file
samtools bam picard dragen
updated by jkbonfield jkbonfield • written by Alex • Alex
0 votes
1 reply
989 views
Integration of NanoString CosMx FOVs
spatial transcriptomics
updated by Bastien Hervé Bastien Hervé • written by solo.albif • solo.albif
0 votes
4 replies
1.5K views
Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid plant assembly
rna-seq
updated by rfran010 • rfran010 • written by Zephy • Zephy
2 votes
8 replies
2.6K views
Cross-species differential gene expression, finding orthologs
orthologs xspecies stringtie differential-expression
written by fe94 • fe94
1 vote
3 replies
1.2K views
Unexpected negative correlation between gene-length and counts
rna-seq bias normalisation
updated by rfran010 • rfran010 • written by Ben • Ben
2 votes
1 reply
764 views
Perturb seq
perturbseq
updated by GenoMax GenoMax • written by shlo12 • shlo12
0 votes
5 replies
3.3K views
Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq ngs pipeline indels snvs
updated by Arup Ghosh Arup Ghosh • written by stuckinanendlessfebruary • stuckinanendlessfebruary
0 votes
1 reply
1.1K views
How important are allele fractions when calling variants?
gatk bacteria bcftools
written by andean • andean
0 votes
0 replies
1.3K views
Job: Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
nucleosomes post_doc cancer_detection generativeai bioinformatics
written by Jakob Skou • Jakob Skou
0 votes
2 replies
2.5K views
Analysing Problem Seen In MEGA X
alignment megax muscle
updated by humarafique.1234 • humarafique.1234 • written by ankurhalder116 • ankurhalder116
0 votes
0 replies
787 views
discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
analysis enrichment
updated by Philip • Philip • written by BobMarleyEnrichment • BobMarleyEnrichment
1 vote
2 replies
1.2K views
DESeq2 outliers-should I be concerned?
deseq2
updated by ATpoint ATpoint • written by bioinfo • bioinfo
0 votes
2 replies
1.2K views
Trimmomatic command
star rnaseq trimmomatic
updated by swbarnes2 swbarnes2 • written by rajdeepboral00 • rajdeepboral00
1 vote
1 reply
1.0K views
Blog: Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
updated by cmdcolin cmdcolin • written by Novogene • Novogene
0 votes
9 replies
2.8K views
Facing issue with output of nextflow pipeline
output nextflow fastqc issue
updated by colindaven colindaven • written by harsh • harsh
0 votes
2 replies
1.8K views
Forum: Pie Charts: to use or not to use
pie-chart graphs
updated by Joe Joe • written by littlebioinformatician • littlebioinformatician
0 votes
1 reply
826 views
Minimum Number of Cells for Downstream Analysis after subsetting a particular cell type (scRNAseq)?
cell single
updated by ATpoint ATpoint • written by Tundup • Tundup
0 votes
3 replies
1.2K views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif ncbi_genome_database acinetobacter_guillouiae nitrogenase nitrogen_fixation
updated by GenoMax GenoMax • written by Nafi • Nafi
0 votes
1 reply
913 views
Target prediction
protien prediction target
updated by dthorbur dthorbur • written by Samprath • Samprath
0 votes
12 replies
3.4K views
Heatmap of a transformed deseq object with pheatmap
deseq2 pheatmap
written by caroline.zanchi • caroline.zanchi
0 votes
0 replies
629 views
CNVkit CNVs call with threshold issues
cnvkit threshold_log2 somatic_variant
written by AIMAR • AIMAR
0 votes
6 replies
2.2K views
PRS result interpretation
risk score prs interpretation polygenic
written by trkfs • trkfs
1 vote
1 reply
933 views
More rare variants than common variants
plink gwas
updated by LChart LChart • written by RT • RT
0 votes
1 reply
978 views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated by Jordan M Eizenga • Jordan M Eizenga • written by gulin • gulin
0 votes
0 replies
1.4K views
Job: Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
ptsd learning bioinformatics deep genomics
written by bjdaigle • bjdaigle
0 votes
4 replies
1.6K views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
replicates omics pooling
updated by LChart LChart • written by sardius • sardius
0 votes
1 reply
1.1K views
Regressing variables for finding Differentially expressed genes
batcheffect seurat bias scrnaseq
updated by Bastien Hervé Bastien Hervé • written by AB AB
0 votes
0 replies
1.3K views
Job: Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany e14
written by elsalatino • elsalatino
1 vote
1 reply
1.3K views
Alternatives to WGCNA
wgcna
updated by LChart LChart • written by Poorvi • Poorvi
0 votes
9 replies
2.4K views
RNA-seq analysis
htseq-count hisat2 featurecounts star
updated by GenoMax GenoMax • written by sk_24 • sk_24
0 votes
2 replies
1.9K views
Liquid Biopsy datasets
rna-seq next-gen liquid biopsy mirna cdna
updated by ehaag • ehaag • written by pacocp • pacocp
0 votes
4 replies
1.9K views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
rna
updated by ehaag • ehaag • written by jimmysibandah • jimmysibandah
0 votes
3 replies
2.1K views
Metagenomics mock datasets
metagenomics
updated by ehaag • ehaag • written by enuhblaise • enuhblaise
3 votes
0 replies
746 views
News: NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics ncbi codeathon
written by MirianT_NCBI • MirianT_NCBI
0 votes
1 reply
999 views
Using structure prediction approaches to predict interaction between two proteins
protein prediction structure
updated by Mensur Dlakic Mensur Dlakic • written by Daniel • Daniel
0 votes
3 replies
1.3K views
How to visualize Combat-seq corrected counts
batch-correction combat-seq
written by as823jk • as823jk
0 votes
6 replies
1.8K views
Single cell expression and accessibility integration using cellxgene data
cellxgene
written by 1769mkc 1769mkc
0 votes
1 reply
993 views
Umbrella pathways in KEGG
kegg r
updated by Arup Ghosh Arup Ghosh • written by Arindam Ghosh Arindam Ghosh
0 votes
2 replies
820 views
Peptide protein dynamics
pepdide
updated by lieven.sterck lieven.sterck • written by venkatramananspd • venkatramananspd
0 votes
4 replies
1.3K views
variant calling chromosome-wise from WGS data
wgs
updated by GenoMax GenoMax • written by Bushra Bibi Bushra Bibi
0 votes
5 replies
1.3K views
Design matrix with uneven patient representation across stages
rna-seq design-matrix limma
written by Lucas • Lucas
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