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0 votes
14 replies
42K views
[main_samview] fail to read the header from sample.bam
alignment
updated by Kevin Blighe Kevin Blighe • written by sambioinfo2018 • sambioinfo2018
8 votes
23 replies
64K views
Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking for family relationships a priori?
plink vcf fam gatk vcftools
updated by Kevin Blighe Kevin Blighe • written by gaelgarcia gaelgarcia
0 votes
1 reply
951 views
TOM matrix WGCNA
wgcna
updated by Kevin Blighe Kevin Blighe • written by frarodmar17 • frarodmar17
0 votes
1 reply
2.0K views
Two-sample Mendelian Randomization (MR) summary statistics
gwas randomization mendelian
updated by Kevin Blighe Kevin Blighe • written by handecadir • handecadir
0 votes
1 reply
1.6K views
Error, 'object too long to compress'
orthologs oma oma
updated by Kevin Blighe Kevin Blighe • written by felix_langschied • felix_langschied
0 votes
1 reply
827 views
KEGG Orthologs (KO) from 16S vs. Metabolites
picrust2 microbiome metabolome
updated by andres.firrincieli andres.firrincieli • written by Arunabh Sharma • Arunabh Sharma
0 votes
1 reply
850 views
Direct RNA-seq Nanopore
drna
updated by Kevin Blighe Kevin Blighe • written by frarodmar17 • frarodmar17
0 votes
5 replies
7.2K views
cellranger mkref fail/error
mkref multiple_species customtranscriptome cellranger transcriptome
updated by Kevin Blighe Kevin Blighe • written by tatsispolychronis • tatsispolychronis
0 votes
2 replies
1.4K views
Using soupX on single nucleus RNA seq data
rnaseq soupx singlenucleus snrnaseq
updated by Kevin Blighe Kevin Blighe • written by happymuffin24 • happymuffin24
0 votes
2 replies
6.0K views
TOPMed Imputation - More than 10000 allele switches
imputation topmed
updated by Kevin Blighe Kevin Blighe • written by Akshaj • Akshaj
0 votes
2 replies
5.5K views
Question regarding batch effect in TCGA-HNSC
cancer deseq2 sva tcga
updated by Kevin Blighe Kevin Blighe • written by Hamada • Hamada
0 votes
0 replies
500 views
BLAST database error while using HiFiAdapterfilt to filter out adapter contaminants from PacBio raw reads
blast pacbio ncbi assembly genome
updated by Kevin Blighe Kevin Blighe • written by pranavdatar01 • pranavdatar01
0 votes
0 replies
6.5K views
rsid in full data table for GSA array but not in the final vcf file
array gsa
updated by Kevin Blighe Kevin Blighe • written by 1769mkc 1769mkc
0 votes
0 replies
6.0K views
Radial plot help
radial-plots bulls-eye
updated by Kevin Blighe Kevin Blighe • written by bioinformatics_rk • bioinformatics_rk
0 votes
3 replies
3.4K views
Forum: Looking for Entry-Level Bioinformatics Project Ideas to Build My Portfolio
bioinformatics genomics next-generation-sequencing
updated by Ram Ram • written by Samudraneel • Samudraneel
0 votes
1 reply
869 views
Is there a difference between signalValue and FoldEnrichment in peak files obtained by MACS2 peakcalling
chip-seq cutandrun
updated by rfran010 • rfran010 • written by sribas.chowdhury888 • sribas.chowdhury888
0 votes
3 replies
1.6K views
ATAC-SEQ FRAGMENT SIZE
size fragment picard atac-seq
updated by ATpoint ATpoint • written by Irene • Irene
0 votes
6 replies
10K views
Statistical test of difference between two conditions and account for the batch
significance-testing test seurat scrna-seq batch
updated by Kevin Blighe Kevin Blighe • written by npont • npont
1 vote
2 replies
9.3K views
Shift in RNA 3' position, Term-Seq vs RNASeq
termseq rnaseq
updated by Kevin Blighe Kevin Blighe • written by npb27 • npb27
0 votes
3 replies
11K views
Automatically annotating a feature using a genbank file
annotation genbank wgs
updated by Kevin Blighe Kevin Blighe • written by Mark • Mark
0 votes
1 reply
6.4K views
Finding RNA genes associated with X protein expression in CITE-seq Seurat object
seq cite single cell
updated by Kevin Blighe Kevin Blighe • written by Picasa Picasa
0 votes
4 replies
2.4K views
using packages with conda
snakemake conda scinkd
updated by Kevin Blighe Kevin Blighe • written by raquel • raquel
0 votes
2 replies
11K views
How to correctly report exon number for CRISPR-Cas9 knockout when genes have multiple isoforms?
numbering exon crispr-cas9
updated by Kevin Blighe Kevin Blighe • written by jakob.vanek • jakob.vanek
0 votes
2 replies
6.5K views
Ribosome profiling
riboseq
updated by Kevin Blighe Kevin Blighe • written by Min So • Min So
0 votes
4 replies
10K views
UMAP QC
scrnaseq spatial transcriptomics umap
updated by Kevin Blighe Kevin Blighe • written by R.L. • R.L.
0 votes
2 replies
1.4K views
Minimap2 segfaults when mapping Nanopore reads to a very large reference database
nanopore minimap2 minimap ont alignment
written by firefox91 • firefox91
0 votes
11 replies
5.3K views
How to use NextFlow to compute identity score between bacterial genomes?
identity score genomes alignment nextflow
updated by Kevin Blighe Kevin Blighe • written by marongiu.luigi marongiu.luigi
0 votes
1 reply
6.8K views
Custom reference sequence length discrepancy with STAR/Salmon/gffread
refseq ensembl fasta star gtf
updated by Kevin Blighe Kevin Blighe • written by ki • ki
0 votes
1 reply
4.4K views
Redox Ratio Analysis - RRApp for MatLab (V 1.3)
rra matlab ratiometric
updated by Kevin Blighe Kevin Blighe • written by bm.nina • bm.nina
0 votes
1 reply
5.4K views
Pfam IsoformSwitchAnalyzerR
isoforms pfam
updated by Ram Ram • written by SpliceAndScript • SpliceAndScript
0 votes
2 replies
6.8K views
Strange pattern in pct_counts_mt from bin2cell deconvolved VisiumHD data
spatial-transcriptomics bin2cell visiumhd
updated by Kevin Blighe Kevin Blighe • written by danielpintard • danielpintard
0 votes
1 reply
2.0K views
Covariate-adjusted SPIEC-EASI
microbiome network spieceasi
updated by Kevin Blighe Kevin Blighe • written by b • b
0 votes
4 replies
15K views
questioning about PCA graph in RNASeq analysis
bioinformatics-rnaseq
updated by Kevin Blighe Kevin Blighe • written by Alaa • Alaa
0 votes
1 reply
5.2K views
BWA alt-aware pipeline troubleshooting
alt-aware bwa samtools
updated by Kevin Blighe Kevin Blighe • written by Duy • Duy
0 votes
3 replies
1.3K views
tximport error (medianLengthOverIsoform)
dtu rna-seq tximport
updated by Kevin Blighe Kevin Blighe • written by LGG • LGG
1 vote
2 replies
1.2K views
Best tool to qc gwas summary stats for a meta analysis
gwas
written by Rangarajan • Rangarajan
0 votes
4 replies
1.3K views
vg giraffe successfully mapped?
vg
updated by colindaven colindaven • written by kingcohn • kingcohn
0 votes
23 replies
4.7K views
Batch Effect
batch effect
updated by Kevin Blighe Kevin Blighe • written by Umair • Umair
0 votes
0 replies
487 views
News: Manual Genome Curation using PretextView course
pretexview genomecuration genomeassembly hic
written by Physalia-courses Physalia-courses
1 vote
2 replies
1.6K views
Merqury QV score evaluation for HiFi assemblies
inspecot hifi qv merqury genome
updated by samuel.a.odonnell samuel.a.odonnell • written by SomeOne • SomeOne
0 votes
4 replies
1.3K views
Can someone please help me understand why my fastq file looks like this?
fastq
updated by GenoMax GenoMax • written by DNAngel DNAngel
0 votes
4 replies
1.1K views
My ChIP-seq mapped reads are not evenly distributed in R1 and R2 fastq file
chip-seq
updated by Ian Ian • written by Pallondyle • Pallondyle
0 votes
1 reply
1.2K views
Error "no rows to aggregate" using makeFunctionalPrediction() Tax4fun2
r tax4fun2 prediction functional makefunctionalprediction
updated by Kevin Blighe Kevin Blighe • written by Marine • Marine
1 vote
2 replies
1.5K views
Slam-Seq Conversion Rate per Read
nf-core slam-seq slamdunk
updated by Kevin Blighe Kevin Blighe • written by Daniel • Daniel
0 votes
10 replies
2.7K views
Errors with RSEM/bowtie2
rna-seq bowtie2 rsem trinity
updated by Kevin Blighe Kevin Blighe • written by Olivia • Olivia
1 vote
1 reply
1.2K views
Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
gatk
updated by Kevin Blighe Kevin Blighe • written by curious curious
0 votes
3 replies
1.4K views
Fst and SNPs
fst r snps ddrad
updated by Kevin Blighe Kevin Blighe • written by md2022 • md2022
1 vote
14 replies
9.6K views
miRNA low mapping ratings
mirna bowtie1 preprocessing counts aligment
updated by Kevin Blighe Kevin Blighe • written by Ant • Ant
0 votes
1 reply
6.4K views
metabolite identification related issue
metabolomics metaboanalyst
updated by Kevin Blighe Kevin Blighe • written by abhisekde038 • abhisekde038
0 votes
4 replies
3.2K views
DNA copy number blacklist for excluding common unreliable regions
blacklist copy number
updated by eebloom • eebloom • written by yura.grabovska • yura.grabovska
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