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0 votes
4 replies
2.2K views
sortmerna not counting the EOF REV file, not working on paired end reads
sortmerna cutadapt
updated by GenoMax GenoMax • written by jway • jway
0 votes
1 reply
926 views
building large dataset transcriptome
de-novo transcriptome
updated by GenoMax GenoMax • written by Raygozak Raygozak
0 votes
0 replies
909 views
DRACH motif enrichment analysis from RNA-seq DEGs
rna-seq motif homer
written by Luca • Luca
0 votes
1 reply
1.1K views
Resolution of ambiguous calls in germline vcf
vcfs germline qc
updated by Jeremy Leipzig Jeremy Leipzig • written by Raygozak Raygozak
0 votes
5 replies
1.9K views
CollectVariantCallingMetrics Error
collectvariantcallingmetrics gatk gvcf
written by Sd • Sd
0 votes
0 replies
944 views
Error in validObject(.Object) : invalid class “ExpressionSet” object: sampleNames differ between assayData and phenoData
gsva
written by Chris • Chris
0 votes
0 replies
686 views
Correct genome version for ncbi37
ensembl biomart
written by ramiro.barrantes • ramiro.barrantes
0 votes
0 replies
981 views
News: The 2024 Canadian Bioinformatics Workshops are here!
cbw workshop training
written by bioinformatics.ca • bioinformatics.ca
0 votes
2 replies
1.1K views
Error from cgat gtf2gtf --method=genes-to-unique-chunks
rna-seq gtf cgat
written by PK • PK
0 votes
2 replies
1.4K views
Choosing right GSEA background gene sets
gsea enrichment analysis
updated by jv jv • written by yxwucq • yxwucq
0 votes
1 reply
1.1K views
Bioinformatic tools to map mutations to pathways
pathway-analysis
updated by Ram Ram • written by eleni.psar • eleni.psar
0 votes
1 reply
1.0K views
Best Freebayes parameter for haploid variant detection
freebayes detection variant
updated by LauferVA LauferVA • written by A_heath • A_heath
0 votes
12 replies
6.5K views
samtools mpileup keeps making an empty file
samtools pileup
updated by anonym101 anonym101 • written by James Reeve James Reeve
2 votes
6 replies
2.5K views
somatic variant calling without matched normal in long-reads
variants cancer illumina ont nanopore
written by eebloom • eebloom
0 votes
3 replies
1.3K views
Protocol to combine WGS with Nanopore for Structural Variant confirmation?
wgs
updated by trausch trausch • written by optimistsso4co3 • optimistsso4co3
1 vote
3 replies
2.0K views
Whole-genome alignment visualization
cactus maf bigmaf
updated by SanjidaR_NCBI • SanjidaR_NCBI • written by gubrins gubrins
0 votes
9 replies
3.3K views
Porechop output?
porechop nanopore
updated by GenoMax GenoMax • written by giulia.trauzzi • giulia.trauzzi
0 votes
2 replies
2.1K views
Downsampling of cells in scRNAseq DE analysis
differential-expression de scrnaseq
updated by Ram Ram • written by mytp • mytp
0 votes
0 replies
545 views
Which fasta file for Variant Calling using RNASeq
rna-seq variant-calling
updated by Ram Ram • written by andrebolerbarros • andrebolerbarros
0 votes
1 reply
712 views
Do I have enough reads for virome analyis?
metagenomics hiseq virome statistics reads
updated by Bruntland Aldre • Bruntland Aldre • written by Mageiros • Mageiros
0 votes
0 replies
527 views
Outputs from FarmCPU (rMPV package)
r farmcpu gwas
written by Noctiluca • Noctiluca
0 votes
4 replies
1.9K views
DESeq2 for two sample conditions
deseq2
updated by Michael Dondrup Michael Dondrup • written by Aaliya • Aaliya
0 votes
1 reply
841 views
DESEQ2 Code
ngs
updated by ATpoint ATpoint • written by ananta.kapoor • ananta.kapoor
0 votes
2 replies
1.4K views
How to parallelize running vg autoindex to create graph references from VCFs with vg?
vg
written by Ricky • Ricky
1 vote
5 replies
5.6K views
WGCNA HeatMap correlating modules and sample conditions
rnaseq heatmap wgcna conditions clustering
updated by GenoMax GenoMax • written by Raito92 Raito92
0 votes
1 reply
1.4K views
Visualizing module eigene relationships in cytoscape
network wgcna cytoscape
updated by Scooter Scooter • written by MARK • MARK
0 votes
2 replies
1.3K views
Alternative tool or website of PathogenFinder
wgs bacteria
updated by GenoMax GenoMax • written by Pegasus • Pegasus
0 votes
2 replies
1.7K views
How I should set `STAR` parameters to keep all the intronic reads?
star mapping
updated by dsull dsull • written by Dan • Dan
0 votes
1 reply
704 views
samsift can't find the AS tag to filter a bam file generated using bowtie2
samsift bowtie2
updated by Pierre Lindenbaum Pierre Lindenbaum • written by michael.flower.14 • michael.flower.14
0 votes
10 replies
7.7K views
PDB residue serial inconsistency and PDB id&UniProt ID mismatch
pdb uniprotid pdbid
updated by Wayne Wayne • written by Nafi • Nafi
0 votes
4 replies
1.4K views
Dsuite Dinvestigate error but no indication as to the source
dsuite
written by Drew • Drew
0 votes
1 reply
2.0K views
getting error when transfer labels for my scRNAseq data using FindTransferAnchors
scrnaseq
written by Sara Sara
0 votes
0 replies
728 views
Discrepancy in Number of SRA between NCBI Website and BigQuery service (SQL request)
ncbi sql bigquery sra
written by marie.harmel • marie.harmel
0 votes
1 reply
973 views
Issue with Image Display and Saving on AgriGO v2 Platform
plants agrigo gene-ontology non-model
updated by Ram Ram • written by Nelo • Nelo
0 votes
5 replies
4.7K views
How to root this tree?
phylogeny tree root
updated by Michael Dondrup Michael Dondrup • written by Mirko • Mirko
0 votes
7 replies
2.9K views
limma eBayes error in analysis of Illumina HumanHT-12 V4.0 expression beadchip data
r beadchip limma microarray illumina
updated by 1769mkc 1769mkc • written by accibio • accibio
0 votes
4 replies
1.9K views
igvShiny issues with loading local bams
r igv shiny
updated by Malcolm.Cook Malcolm.Cook • written by genya35 • genya35
0 votes
2 replies
1.3K views
Granges manipulation
granges
written by Bastien Hervé Bastien Hervé
1 vote
3 replies
1.6K views
Practical Haplotype Graph
methodid phg
updated by lcj34 lcj34 • written by yifangt86 • yifangt86
0 votes
0 replies
588 views
Choosing TPM cutoff for PCR validation
pcr tpm
written by sleepystudent • sleepystudent
0 votes
4 replies
3.4K views
Manhattan plot for TWAS results
twas gwas manhattan-plot
written by rheab1230 • rheab1230
0 votes
3 replies
2.0K views
HLA genotyping of whole genome sequencing data
hla genotyping wgs
written by Biomed-jeh • Biomed-jeh
0 votes
0 replies
679 views
Building Ensembl database for HMMER
hmmer
updated by Ram Ram • written by J • J
0 votes
1 reply
1.3K views
Multiple replicates with one SoapDenovo-Trans run?
rna-seq soapdenovo-trans transcriptome
updated by nargisbashir10 • nargisbashir10 • written by nina.maryn • nina.maryn
1 vote
1 reply
1.9K views
gene alignment (microsynteny)
alignment microsynteny
updated by cmdcolin cmdcolin • written by gubrins gubrins
0 votes
0 replies
818 views
Any tool that can give me a list of DNA/RNA aptamers against specific protein as the in vitro SELEX library to screen the sequences?
aptamer protein selex
written by J.F.Jiang J.F.Jiang
0 votes
2 replies
1.1K views
Deseq2 shows differential expression while TPM values are not significantly different
deseq2 tpm
updated by jv jv • written by Aiswarya • Aiswarya
1 vote
1 reply
992 views
ATAC-seq downstream analysis
atac-seq diffbind
updated by ATpoint ATpoint • written by maplewj • maplewj
1 vote
7 replies
2.7K views
Selecting query format for repeated calls to NCBI's API
ncbi esummary elink api efetch
updated by GenoMax GenoMax • written by LauferVA LauferVA
0 votes
0 replies
661 views
Predictor of Activation Domains
protein domain
written by buhbs • buhbs
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