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0 votes
2 replies
1.2K views
Need a spatial transcriptomics cancer data
ngs scrna-seq single-cell
updated by jv jv • written by ahmad mousavi ahmad mousavi
0 votes
2 replies
924 views
Filtering the SNPs
gwas snp gbs
updated by dthorbur dthorbur • written by umeshtanwar2 • umeshtanwar2
2 votes
3 replies
1.5K views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated by Darked89 Darked89 • written by ebaldwin • ebaldwin
0 votes
0 replies
567 views
News: Online course: Computation Tumor Evolution
r cancer-genomics tumor-evolution genomics
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
0 replies
549 views
Interpreting HOMER getDifferentialPeaks.pl output columns
atacseq
written by Ronin • Ronin
0 votes
3 replies
1.1K views
BLAST
dna blast sequencing
updated by GenoMax GenoMax • written by m90 • m90
0 votes
2 replies
1.5K views
How to choose --hwe threshold?
plink hardy-weinberg quality-control qc
written by _quantum_girl_ • _quantum_girl_
0 votes
3 replies
1.3K views
Why statistic test should I use?
statistics
updated by dariober dariober • written by Matheus • Matheus
1 vote
7 replies
4.3K views
Shrink logFC values after edgeR
logfc edger
updated by Gordon Smyth Gordon Smyth • written by arvind.1 • arvind.1
0 votes
4 replies
1.4K views
Batch effect
single-cell seuratv5 seurat
written by f-bee • f-bee
0 votes
7 replies
1.9K views
1000 Genome: Cause of duplicate variants with different genotypes
crossmap 1000genome 1000g
updated by Giulio Genovese • Giulio Genovese • written by JourneyToAbyss JourneyToAbyss
0 votes
7 replies
3.5K views
cellranger count error
single-cell cellranger
updated by GenoMax GenoMax • written by Elinor • Elinor
0 votes
0 replies
563 views
difference in class code between cuffcompare and cuffmerge
cuffmerge lncrna cufflinks cuffcompare
written by ZZOYEA • ZZOYEA
0 votes
2 replies
1.3K views
How to exclude reads from a fastq file, using a list of read names?
fastq grep filter
written by Tash • Tash
0 votes
1 reply
1.2K views
"N/A" in fgsea result
gsea fgsea
updated by Dave Carlson Dave Carlson • written by puffpumpkin • puffpumpkin
0 votes
0 replies
903 views
How is the "fold change over control" bigwig file generated from ATAC-seq data?
atac-seq encode control
written by Ruoyun • Ruoyun
0 votes
5 replies
2.1K views
Trouble Understanding DESeq2 Design Formula ("Model Matrix is not Full Rank")
deseq2 biomarkers 16s
written by Rachel • Rachel
1 vote
6 replies
2.8K views
Differential expression analysis with very high duplication rate
rna-seq de picard pcr duplicates
written by JMB • JMB
0 votes
3 replies
2.0K views
FASTQ-DUMP error while downloading HGDP datadset
hgdp fastqdump
written by Qboy • Qboy
1 vote
4 replies
5.4K views
GFF3 to 12-column BED
gff3 bed
updated by Ram Ram • written by New2R • New2R
1 vote
10 replies
20K views
conversion of GFF3 formate to BED format
rna-seq
updated by Ram Ram • written by blooming.daisy333 • blooming.daisy333
1 vote
0 replies
1.4K views
Tool: gxf2bed: A high-performance GTF/GFF-to-BED converter written in Rust
convert gff gtf bed
written by alejandrogzi • alejandrogzi
0 votes
4 replies
1.6K views
Strategies with annotated VCF files to filter very big VCF from WGS
wgs vcf whole-genome-sequencing
updated by barslmn • barslmn • written by randyOrlando • randyOrlando
1 vote
3 replies
2.8K views
GTEx TPMs Vs normalized data
gtex rna-seq normalization gene-expression
updated by jv jv • written by DS • DS
2 votes
11 replies
6.7K views
Nextflow - I/O and index issues
bwa-mem2 groovy dsl nextflow trim-galore
written by bhumm • bhumm
0 votes
6 replies
1.5K views
Find Large-scale CNVs in whole exome sequencing
wes scrna-seq cnv
written by fifty_fifty • fifty_fifty
1 vote
7 replies
2.1K views
Did the stability of the transcriptome be affected by factors such as pathological conditions, diet?
transcriptome
updated by Yogi • Yogi • written by GrantS • GrantS
0 votes
0 replies
666 views
News: Course live online Intro Bayesian Analyses, March 4-8, 2024
r python bayesian
written by Sole • Sole
0 votes
2 replies
1.1K views
Extracting mutation information from a VCF file.
biopython vcf phylogenetic usher
updated by Pierre Lindenbaum Pierre Lindenbaum • written by realtreeecat • realtreeecat
0 votes
1 reply
595 views
De-novo transcriptome
de-novo
updated by Ram Ram • written by bala • bala
0 votes
7 replies
2.3K views
Three fastq files
fastq sra cellranger
updated by swbarnes2 swbarnes2 • written by charms.charms • charms.charms
0 votes
4 replies
1.4K views
How to fix DESeq2 Error in checkFullRank(modelMatrix)
deseq2
updated by i.sudbery i.sudbery • written by marco.barr • marco.barr
0 votes
3 replies
1.2K views
Can I run a blast for each contig in my contigs file?
blast
updated by GenoMax GenoMax • written by roberto.bonnellya • roberto.bonnellya
0 votes
1 reply
1.2K views
How to make separate plots in Monocle3 using combined control and treatment samples
monocle3 plot_cells
updated by Ram Ram • written by alwayshope • alwayshope
0 votes
0 replies
442 views
Set pentanucleotide context in dndscv
dndscv
written by vswamy • vswamy
0 votes
6 replies
2.3K views
GO and KEGG
go bulk-rna-seq rstudio kegg
updated by jv jv • written by matteo.levorato • matteo.levorato
0 votes
2 replies
829 views
Internal controls/ Reference Samples for Nanopore
nanopore
updated by dthorbur dthorbur • written by pixie@bioinfo pixie@bioinfo
0 votes
3 replies
1.7K views
Merge seurat list
merge
updated by GenoMax GenoMax • written by Long • Long
0 votes
1 reply
938 views
What could be a better K-mer for my WGS assembly task using ABySS, with my current hardware profile.
abyss genome k-mer assembly
updated by shelkmike shelkmike • written by Vijith • Vijith
0 votes
3 replies
1.2K views
How to show that correlation from one method is more significant than other method?
p-value model-performance significance correlation
updated by Shred Shred • written by rheab1230 • rheab1230
0 votes
2 replies
1.4K views
Pymol movie - ligand and receptor binding.
pymol protein structure pdb
written by Hansen_869 • Hansen_869
0 votes
1 reply
1.3K views
CNVKit .cnr to cns conversion algorithm
cnvkit cnv
updated by francisco • francisco • written by Jade • Jade
0 votes
4 replies
2.6K views
How can I call somatic CNV in tumor samples with no normal samples?
r cnvkit copy-number ascat
updated by francisco • francisco • written by Saurabh • Saurabh
0 votes
4 replies
3.0K views
Creating a csv in a specific format from FASTQ file names
nf-core bash
updated by Mahmoud.Abdallah • Mahmoud.Abdallah • written by jamie3355 • jamie3355
1 vote
7 replies
12K views
Remove adaptaters from ONT reads : An alternative to Porechop ?
minion promethion porechop nanopore ont oxford
updated by Michael Dondrup Michael Dondrup • written by Rox Rox
0 votes
3 replies
3.1K views
How I can get percent identity matrix from clustalw or clustalo?
clustalo clustalw msa multiplesequencealignment pairwise
written by Jiun • Jiun
0 votes
2 replies
1.8K views
What is the best GWAS tool to use for a very large cohort data (UK Biobank data)?
bolt-lmm gwas regenie saige hail
updated by GenoMax GenoMax • written by lsy9 • lsy9
0 votes
7 replies
2.2K views
Split large deletion D in CIGAR string and filtering reads
cigar reads
updated by Pierre Lindenbaum Pierre Lindenbaum • written by marco.barr • marco.barr
0 votes
2 replies
1.3K views
How to do DESeq2 on Kallisto Data
unfolded kallisto deseq2 reponse protein
updated by dsull dsull • written by Aaliya • Aaliya
0 votes
1 reply
1.0K views
Conversion Issue with bcl2fastq2
bcl2fastq2 novaseq6000
updated by Ram Ram • written by Christopher • Christopher
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