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0 votes
9 replies
3.9K views
Adding CB tag to bam file
samtools bam
written by Maria • Maria
0 votes
2 replies
1.7K views
AGeNT LocatIt
agent locatit wes umi duplicates
updated by barslmn • barslmn • written by jhy • jhy
0 votes
5 replies
1.5K views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated by GenoMax GenoMax • written by Bertalan_Takacs • Bertalan_Takacs
0 votes
0 replies
559 views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
tcga gdcprepare
updated by Ram Ram • written by glaciya2018 • glaciya2018
0 votes
0 replies
1.0K views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome pgap ncbi roary prokka
written by pramach1 • pramach1
0 votes
13 replies
6.5K views
Tax4Fun2 - error
tax4fun silva blast
updated by drstalinantony28 • drstalinantony28 • written by ymj • ymj
0 votes
1 reply
1.0K views
GEMMA GWAS how to specify factor or numerical for covariates
covariate gemma gwas
updated by Sofia • Sofia • written by mawigoj318 • mawigoj318
0 votes
0 replies
695 views
Sequence BLAST in plus/minus and plus/plus
blast crispr strand sequencing
written by Sergio A.S. • Sergio A.S.
0 votes
7 replies
2.4K views
To get p-values for the TPM
p-value tpm rsem
updated by dsull dsull • written by VITALA • VITALA
0 votes
5 replies
1.9K views
different FeatureCounts output for the same data
fpkm counts rsubread rna-seq
updated by Istvan Albert Istvan Albert • written by sehriban.buyukkilic • sehriban.buyukkilic
0 votes
0 replies
859 views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated by Ram Ram • written by newuser2024 • newuser2024
0 votes
2 replies
996 views
alignment result
rna-seq samtools hisat2
written by ahmad.sajad4541 • ahmad.sajad4541
0 votes
0 replies
557 views
News: hands-on introduction to generalized linear models (GLMs) using R
generalized-linear-models glm r
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
2 replies
1.4K views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scrnaseq
written by mropri mropri
0 votes
2 replies
989 views
HaplotypeCaller - only SNPs
haplotypecaller gatk
updated by Bushra Bibi Bushra Bibi • written by lorena9132 • lorena9132
0 votes
0 replies
756 views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy anndata numpy
written by Kash Kash
0 votes
2 replies
1.4K views
Gene set enrichment analysis differences between 2020 and 2024
gene-ontology
updated by geneontologyhelp • geneontologyhelp • written by catherine.teyssier • catherine.teyssier
0 votes
1 reply
750 views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting blast
updated by Istvan Albert Istvan Albert • written by Abeer • Abeer
0 votes
4 replies
2.3K views
Should I use unpaired reads from trimmomatic
rna-seq qc trimmomatic
updated by swbarnes2 swbarnes2 • written by dxj294 • dxj294
0 votes
1 reply
801 views
How to solve this RoseTTAFold colaboratory error?
modeling google colaboratory rosettafold protein
updated by Mensur Dlakic Mensur Dlakic • written by benguyarenbeyaz98 • benguyarenbeyaz98
0 votes
2 replies
1.1K views
How to calculate identity percentage between proteins contained in a FASTA file?
protein fasta alignment
updated by Ram Ram • written by v.berriosfarias • v.berriosfarias
0 votes
1 reply
2.3K views
Seurat merge and batch correction
seurat
updated by Ram Ram • written by sooni • sooni
1 vote
1 reply
1.2K views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Biostar Biostar
0 votes
1 reply
821 views
Including plasmid in alignment
bacteria transcriptomics bowtie2 star
written by heelpPlease • heelpPlease
0 votes
9 replies
2.2K views
TCGA2STAT Error: Firehose connection
firehose tcga
updated by LauferVA LauferVA • written by Gnana • Gnana
0 votes
1 reply
1.6K views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scrnaseq
updated by bk11 • bk11 • written by alphaflylizard • alphaflylizard
0 votes
3 replies
1.3K views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated by Istvan Albert Istvan Albert • written by Dylan • Dylan
2 votes
5 replies
2.2K views
How to trim transcripts using information from NCBI contamination screen report
rnaseq assembly transcriptome contamination
written by Lada • Lada
0 votes
11 replies
3.1K views
Redirection of Duplicate PMIDs
pubmed pmid
updated by LauferVA LauferVA • written by dominickd • dominickd
0 votes
16 replies
4.7K views
How to convert plink files to Hapmap Format
gwas plink
updated by bk11 • bk11 • written by Sofia • Sofia
0 votes
0 replies
568 views
The concept of co-occurrence network structure
co-occurence microbiome network
written by ohtang7 • ohtang7
3 votes
0 replies
585 views
News: Interested in Spatial Omics?
bioconductor spatial-omics spatial-transcriptomics
updated by Ram Ram • written by Physalia-courses Physalia-courses
1 vote
2 replies
1.6K views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated by Pierre Lindenbaum Pierre Lindenbaum • written by AshleeThomson • AshleeThomson
0 votes
1 reply
766 views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs methylkit
updated by GenoMax GenoMax • written by Srinka • Srinka
4 votes
5 replies
10K views
ISCN annotation for SV/CN VCF files
sv
updated by princessmaryanabdullahi • princessmaryanabdullahi • written by a.beggs • a.beggs
0 votes
5 replies
1.8K views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 grch38 assembly
written by njornet • njornet
2 votes
4 replies
3.4K views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
written by kirillkirilenko • kirillkirilenko
0 votes
0 replies
536 views
Software to calculate RSCU, ENC other than codonw
rscu codonw
updated by Ram Ram • written by SHREYA • SHREYA
0 votes
3 replies
1.7K views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated by colindaven colindaven • written by rj.rezwan • rj.rezwan
0 votes
0 replies
642 views
Merging replicates from Encode project
chip-seq encode
written by Nurken • Nurken
1 vote
3 replies
1.3K views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
written by WouterDeCoster WouterDeCoster
0 votes
3 replies
969 views
Help for coding: Trinity for differential gene expression studies
gene
updated by mchour • mchour • written by rhossen • rhossen
0 votes
1 reply
1.5K views
WGCNA preservation analysis
wgcna preservation
updated by Michael Dondrup Michael Dondrup • written by michael.flower.14 • michael.flower.14
0 votes
4 replies
1.7K views
some error in building kraken2 database
metagenome kraken2
updated by GenoMax GenoMax • written by Art1ess • Art1ess
0 votes
1 reply
1.6K views
Subset Seurat object from Xenium spatial data
seurat xenium spatial
updated by bk11 • bk11 • written by Susmita Mandal Susmita Mandal
0 votes
1 reply
1.7K views
Plots for DNA methylation data
plots dna methylation
updated by GenoMax GenoMax • written by sarahawan92 • sarahawan92
0 votes
3 replies
1.7K views
python file for coding potential calculator
cpc2.py
updated by atharvakarkare14 • atharvakarkare14 • written by Ashok • Ashok
0 votes
1 reply
720 views
Failed kmer content
kmer illumina ngs
updated by Ram Ram • written by Kasturi • Kasturi
0 votes
0 replies
724 views
Forum: Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation scrna llm
written by yxwucq • yxwucq
0 votes
0 replies
517 views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
hmmcopy copy-number-analysis r
updated by Ram Ram • written by SSSJec • SSSJec
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