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0 votes
0 replies
734 views
News: Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
genotype-likelihoods low-coverage population-genomics angsd
updated by Ram Ram • written by Physalia-courses Physalia-courses
0 votes
2 replies
913 views
How to decrease the motif score?
motif-score
updated by Ram Ram • written by Hadia • Hadia
0 votes
0 replies
506 views
immuCell Abundance infiltrate
immucell
updated by Ram Ram • written by elbakri.fatimazahrae • elbakri.fatimazahrae
0 votes
2 replies
1.2K views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scrna-seq
updated by LauferVA LauferVA • written by carolofharvest • carolofharvest
0 votes
0 replies
834 views
MaxEntScan for rMATS results
maxentscan rmats
written by adi.gershon1 • adi.gershon1
0 votes
0 replies
1.1K views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not appear to be correct. E.g it does not contain a 'Lib
repeatmasker. maker. annotation.
written by Sony Nguyen • Sony Nguyen
0 votes
2 replies
1.5K views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq stringtie salmon
updated by Ram Ram • written by Tonya S. • Tonya S.
1 vote
4 replies
2.7K views
Tool: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
novademux novaseq illumina demultiplexing barcode
written by Brian Bushnell Brian Bushnell
0 votes
11 replies
7.7K views
ComplexHeatmap - How to change fontsize of rowAnnotation
r complexheatmap
updated by Ram Ram • written by hannes.bongartz • hannes.bongartz
0 votes
2 replies
1.3K views
perl Error - needLargeMem Bigwig
bigwig perl mitosalt
written by marco.barr • marco.barr
0 votes
0 replies
618 views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
written by niconps14 • niconps14
0 votes
5 replies
1.8K views
How to scrape BioMart data from https://sorfs.ugent.be/ website
biomart
updated by Pierre Lindenbaum Pierre Lindenbaum • written by QX • QX
0 votes
6 replies
4.8K views
Harmony integration group.by.var parameter
single-cell harmony
updated by jared.andrews07 jared.andrews07 • written by Picasa Picasa
1 vote
1 reply
1.9K views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
af gnomad snp
updated by Jeremy Leipzig Jeremy Leipzig • written by liaotsungjen • liaotsungjen
0 votes
0 replies
675 views
Exon Annotation failed using homer annotatePeaks.pl
homer alternative-splicing annotatepeaks
updated by Ram Ram • written by Alessia • Alessia
1 vote
4 replies
2.3K views
How to calculate cell type frequency between two groups in single cell data
seurat single-cell sc-rna cell-type
updated by Francesco • Francesco • written by Sara • Sara
0 votes
4 replies
1.4K views
Mutation counts corrected by number of samples
mutations wes genomics wgs
written by garcesj • garcesj
0 votes
1 reply
4.2K views
bfctools merge [E::hts_open_format] Failed to open file
snp
updated by Ram Ram • written by andemexoax • andemexoax
0 votes
1 reply
995 views
LDhat lookup table
ldhat
updated by Ram Ram • written by Matteo • Matteo
0 votes
0 replies
639 views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
polygenic-risk-score imputation
updated by Ram Ram • written by kl • kl
0 votes
5 replies
1.6K views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
bowtie
written by Deepthi • Deepthi
0 votes
4 replies
2.0K views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
updated by Ram Ram • written by TNF_alpha • TNF_alpha
0 votes
2 replies
1.7K views
Overlapping clusters for different biological conditions: Seurat, UMAP
seurat scrna-seq umap
written by bio_info • bio_info
2 votes
4 replies
9.0K views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-rna
updated by fracarb8 fracarb8 • written by txema.heredia • txema.heredia
0 votes
0 replies
612 views
R code for KEGG pathways output
keggrest dplyr kegg r
written by doramora • doramora
0 votes
1 reply
755 views
finding highly divergent orthologs using exonerate
ortholog exonerate evolution
updated by dthorbur dthorbur • written by Emily • Emily
0 votes
3 replies
1.5K views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
nucleotidediversity mtdna pacbio
written by hashim.rana11 • hashim.rana11
0 votes
1 reply
577 views
Does prokka work the same on forward and reverse complementary reads?
prokka
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Maksim • Maksim
0 votes
2 replies
1.1K views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
plink gwas snp
written by F110152169 • F110152169
0 votes
10 replies
4.8K views
Venter Genome Vcf
vcf
updated by Jeremy Leipzig Jeremy Leipzig • written by win win
0 votes
0 replies
627 views
16S analysis for specie of bacteria identification
species-identification 16s kraken2
updated by Ram Ram • written by Christopher • Christopher
0 votes
0 replies
717 views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated by GenoMax GenoMax • written by jway • jway
0 votes
3 replies
1.5K views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell rna-seq single
updated by ATpoint ATpoint • written by shahzaibali • shahzaibali
0 votes
2 replies
1.3K views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
macs2 atacseq diffbind
written by atan • atan
0 votes
2 replies
1.3K views
What do the transcript variant # mean in RefSeq?
refseq
updated by Ram Ram • written by curious curious
0 votes
7 replies
3.5K views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body expression atlas
updated by ATpoint ATpoint • written by Shicheng Guo Shicheng Guo
1 vote
3 replies
1.6K views
Error when looping over multiple columns in a data frame in R
statistics r
updated by Jeremy • Jeremy • written by Mohamed Samir • Mohamed Samir
2 votes
0 replies
1.3K views
Job: Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
genomics sequencing sweden stockholm scilifelab
written by Matthias Zepper Matthias Zepper
0 votes
1 reply
631 views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
beast2.5 fossil
updated by Ram Ram • written by a.bibek52 • a.bibek52
1 vote
7 replies
7.9K views
Difference in Bismark output methylation call files and coverage files
rrbs bismark dna-methylation
updated by Papyrus Papyrus • written by linelr • linelr
3 votes
2 replies
1.3K views
Job: 2 PhD Students in single-cell bioinformatics
phd genomics single-cell ngs
written by mtabaka • mtabaka
0 votes
1 reply
1.0K views
minfi::getQC - badsamplecutoff 10.5
getqc minfi methylation epicv2
updated by Papyrus Papyrus • written by June • June
0 votes
2 replies
1.8K views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc ewas minfi
updated by June • June • written by rkb965 • rkb965
1 vote
6 replies
1.7K views
Error with BiocParallel. No barcodes files found
barcodes scrna-seq singlecellexperiment
written by bio_info • bio_info
0 votes
3 replies
1.3K views
Unexpected read length from NGS
ngs illumina
written by QX • QX
0 votes
7 replies
2.9K views
samtools write-index
samtools
written by R.L. • R.L.
0 votes
3 replies
1.7K views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie quantification
written by Varsha • Varsha
0 votes
2 replies
1.2K views
How to interpret this plotMDS of three disease clusters?
microarray plotmds degs
updated by ATpoint ATpoint • written by egascon • egascon
0 votes
0 replies
504 views
GWAS or QTL mapping in RIL population
gwas ril
written by 韩雨 • 韩雨
0 votes
0 replies
545 views
VEP annotation tool: "." isn't numeric in addition (+)
vep vcf
updated by Ram Ram • written by emma.a • emma.a
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