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1 vote
2 replies
1.5K views
Difference between mapping quality and minimum base quality
freebayes
written by A_heath • A_heath
0 votes
10 replies
3.4K views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf gatk vcf genomics mutect2
updated by GenoMax GenoMax • written by Samuel • Samuel
0 votes
5 replies
2.0K views
UMI_extract for paired end reads of micro_RNA
umi-tools umi mirna
updated by ATpoint ATpoint • written by otieno43 • otieno43
0 votes
5 replies
1.8K views
how to convert SummarizedExperiment files to DESeqDataSet??
scrna-seq deg deseq2
updated by Haci Haci • written by kayah • kayah
0 votes
6 replies
3.6K views
Convert Gene symbol to Ensembl ID
mygene
updated by Alex Reynolds Alex Reynolds • written by r.shiasi3897 • r.shiasi3897
24 votes
46 replies
21K views
Tool: ChatGPT optimized for bioinformatics questions
gpt
updated by LauferVA LauferVA • written by Sasha Sasha
0 votes
3 replies
1.3K views
quality control scRNAseq
scrnaseq qc
updated by jv jv • written by sarahmanderni sarahmanderni
0 votes
4 replies
6.2K views
conda install -Killed
conda
written by marco.barr • marco.barr
0 votes
1 reply
1.3K views
Detecting presence of UMI from BAM/fastq files without prior knowledge
fastq bam picard sequencing
updated by i.sudbery i.sudbery • written by artemd • artemd
0 votes
4 replies
1.4K views
BLAST parameters for sequences with high similarity
blast sanger 16s v4 miseq
updated by GenoMax GenoMax • written by behzad.karkaria • behzad.karkaria
0 votes
3 replies
1.6K views
Reformatting Merged and Unmerged Paired-End Files
illumina fastp fastqc bbmap
updated by GenoMax GenoMax • written by young_bioinformatician young_bioinformatician
0 votes
1 reply
1.1K views
ColabFold
colabfold
updated by dthorbur dthorbur • written by Preeti • Preeti
1 vote
0 replies
1.1K views
News: Learn how to create robust bioinformatics pipelines for reproducible and comparable NGS analyses
nextflow pipeline workshop
written by David Langenberger David Langenberger
0 votes
0 replies
627 views
SAMstat mapping quality report MAPQ gt vs MAPQ lt
sequencing mapping samstat
written by njornet • njornet
0 votes
3 replies
1.3K views
I can't add VAF from population for all of my variants from VCF file
genomics vcf gnomad
updated by Ram Ram • written by Samuel • Samuel
0 votes
2 replies
1.1K views
VCF file transfer to a better genome
vcf
updated by colindaven colindaven • written by Nilo • Nilo
0 votes
7 replies
2.0K views
Pan genome of genes
get_homologues
updated by b.contreras.moreira • b.contreras.moreira • written by Pedro • Pedro
0 votes
1 reply
1.1K views
Get_Homologues
get_homologues homologues clusters
updated by b.contreras.moreira • b.contreras.moreira • written by utkarsh.sood • utkarsh.sood
0 votes
5 replies
2.0K views
Tutorial for analyzing WGBS data
ngs methylseq wgbs
written by pt.taklifi pt.taklifi
0 votes
4 replies
1.2K views
Some questions about bulk RNA-seq data normalization
rna-seq ngs bulk normalize
written by feather-W • feather-W
0 votes
4 replies
1.3K views
repeatseq compilation issues
ngs repeats repeatseq repeatexpansion genomics
updated by Michael Dondrup Michael Dondrup • written by adarsh • adarsh
1 vote
1 reply
974 views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
complexheatmap
written by CTLong • CTLong
0 votes
0 replies
633 views
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
spades unmapped_reads. assembly. masurca.
written by Sony Nguyen • Sony Nguyen
0 votes
2 replies
1.0K views
how to run multiple bam files for CNVkit input
annotation bam cnvkit
written by Dora • Dora
0 votes
2 replies
1.1K views
Stringtie error: Error: input file –e cannot be found!
rna-seq tuxedo stringtie transcriptomics
written by menyawino • menyawino
0 votes
0 replies
547 views
MG-RAST KEGG KO Search
mg-rast kegg metagenomics ko
written by Jeremy • Jeremy
0 votes
3 replies
1.3K views
Demonstrating lack of difference between two peaksets
diffbind chip-seq
updated by LauferVA LauferVA • written by Aspire Aspire
0 votes
6 replies
1.9K views
biological meaning /summary for similar sets of GO terms
annotation go
updated by Istvan Albert Istvan Albert • written by lessismore lessismore
2 votes
2 replies
2.0K views
What is the meaning of miniasm -2S6 command?
oxford-nanopore miniasm assembly
updated by Ram Ram • written by traditionalGuy • traditionalGuy
0 votes
5 replies
1.6K views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
kegg entrez ensembl
written by Maxwell • Maxwell
0 votes
9 replies
2.4K views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases python primers biopython
updated by Dave Carlson Dave Carlson • written by Matthew • Matthew
0 votes
4 replies
1.6K views
Is it feasible to merge Illumina RNA-Seq data with varying read lengths?
illumina rna-seq paired-end
updated by i.sudbery i.sudbery • written by mathavanbioinfo mathavanbioinfo
0 votes
0 replies
619 views
MIRA runs yielding different assemblies with same input data and parameters
mira replication denovo assembly
written by btc347 • btc347
0 votes
1 reply
812 views
Understanding Uncommon Genotype Formats in VCF Files Generated by nf-core RNAvar Pipeline
genotype rnaseq
updated by Pierre Lindenbaum Pierre Lindenbaum • written by ASid • ASid
0 votes
2 replies
2.0K views
Seurat: CreateSeuratObject error, please help
seruat
written by mnx0723 • mnx0723
0 votes
2 replies
2.3K views
ggplot2 installation
ggplot2
updated by rpolicastro rpolicastro • written by safeassli • safeassli
0 votes
1 reply
838 views
How to perform enrichment p-value for a motif
enrichment statistics
updated by Trivas • Trivas • written by Apex92 • Apex92
0 votes
3 replies
1.4K views
Corset error reading input files
corset
updated by Ram Ram • written by scarey • scarey
0 votes
5 replies
1.1K views
Merging bam files from different runs
samtools bam
updated by GenoMax GenoMax • written by shpak.max • shpak.max
0 votes
0 replies
425 views
edgeR paired analysis with three conditions
edger
written by suraj • suraj
3 votes
0 replies
1.0K views
Herald: The Biostar Herald for Monday, March 11, 2024
herald
written by Biostar Biostar
0 votes
5 replies
2.0K views
Bedtools getfasta: error
getfasta bedtools
updated by GenoMax GenoMax • written by ummeswaiba • ummeswaiba
0 votes
2 replies
1.1K views
RNA-seq DE with AAV injection
aav rna-seq edger enrichment
updated by rpolicastro rpolicastro • written by CriticalP • CriticalP
0 votes
1 reply
1.2K views
DMRcate for sequencing data
dmrcate dna-methylation differential-methylation
updated by Basti • Basti • written by alejandrarodrigu21 • alejandrarodrigu21
0 votes
0 replies
746 views
How can I conduct a meta-analysis of RNA-seq or microarray data?
r rna-seq microarray meta-analysis
written by wyt1995 • wyt1995
0 votes
2 replies
1.6K views
Query Name too long - samtools
samtools
updated by GenoMax GenoMax • written by marco.barr • marco.barr
0 votes
0 replies
600 views
News: Online course: Genome Assembly and Annotation - 3 seats left
genome-assembly galaxy genome-annotation
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
1 reply
658 views
Computing the neighborhood graph in single cell pipeline
single-cell knn
updated by ATpoint ATpoint • written by QX • QX
0 votes
5 replies
1.9K views
Is it appropriate to publish a phylogenetic tree with low basal bootstarp value
dna tree phylogenetic
updated by Joe Joe • written by zhou03091010 • zhou03091010
0 votes
5 replies
1.9K views
Is it necessary to sort fastq files by sequence before running variant analysis?
fastq ngs sort
updated by GenoMax GenoMax • written by SlowSD • SlowSD
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