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697 results • Page 3 of 14
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0
votes
2
replies
165
views
CreateSeuratObject taking very long
seurat
6 hours ago by eae6d2e7 • 0
1
vote
2
replies
212
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
3 days ago by ojaswinipandey • 0
1
vote
4
replies
303
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA whole-genome-sequencing NCBI
updated 3 days ago by 44k • written 3 days ago by • 0
2
votes
4
replies
243
views
Filter Genome for Specific Sites
bedtools
updated 3 days ago by 44k • written 3 days ago by • 0
0
votes
3
replies
256
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 3 days ago by ▴ 130 • written 4 days ago by ▴ 30
1
vote
1
reply
130
views
Generating Group/Cluster Lists from fastq files
Sequencing RNA-seq DNA-Seq
updated 3 days ago by 142k • written 3 days ago by • 0
0
votes
0
replies
100
views
News: Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor Systems-Biology Network-Analysis R
updated 3 days ago by 44k • written 3 days ago by ★ 2.5k
2
votes
0
replies
138
views
Herald: The Biostar Herald for Monday, May 20, 2024
herald
3 days ago by Biostar 2.8k
3
votes
5
replies
440
views
Super ehancers
enhancers
updated 2 days ago by ★ 17k • written 22 days ago by • 0
0
votes
2
replies
183
views
vcf phasing
beagle WhatsHap phasing
2 days ago by safeassli ▴ 10
0
votes
2
replies
211
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r Upset
3 days ago by sainavyav22 • 0
0
votes
1
reply
610
views
Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 3 days ago by ▴ 40 • written 8 months ago by • 0
1
vote
2
replies
194
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 3 days ago by 44k • written 4 days ago by ▴ 10
0
votes
3
replies
210
views
GATK Structural Variants Pipeline - Steps
SV GATK Variant-Calling
updated 3 days ago by 44k • written 4 days ago by ▴ 20
0
votes
0
replies
100
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat single-cell scRNA-seq
updated 3 days ago by 44k • written 3 days ago by ▴ 20
0
votes
1
reply
144
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy GO R
updated 3 days ago by ▴ 130 • written 4 days ago by ▴ 20
0
votes
1
reply
110
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 3 days ago by 142k • written 4 days ago by • 0
0
votes
0
replies
178
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 3 days ago by 44k • written 4 days ago by ▴ 20
0
votes
0
replies
105
views
transcriptome annotation
annotation trinity transcriptome
updated 3 days ago by 44k • written 4 days ago by • 0
0
votes
5
replies
237
views
Why most genes have high padj values
RNA-seq DEG
updated 3 days ago by 44k • written 4 days ago by • 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 4 days ago by ▴ 30 • written 3.1 years ago by • 0
0
votes
1
reply
151
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 4 days ago by 11k • written 4 days ago by • 0
0
votes
4
replies
259
views
GO analysis: p-value range
GO R
updated 3 days ago by 4.6k • written 4 days ago by ▴ 20
1
vote
2
replies
236
views
News: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk PlatformPresentation offtopic
updated 3 days ago by 6.4k • written 4 days ago by • 0
1
vote
3
replies
249
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq seqtk extractionproblem
updated 3 days ago by 142k • written 5 days ago by • 0
0
votes
0
replies
104
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R Mean Affymetrix Probes Grouping
4 days ago by Maryam • 0
0
votes
4
replies
349
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
4 days ago by Bibi • 0
1
vote
2
replies
359
views
is there a tool to recover corrupted fastq files
fastq short-read
updated 4 days ago by • 0 • written 3 months ago by ▴ 60
0
votes
0
replies
116
views
handling bio replicates for chromHMM
replicates chromHMM
4 days ago by Hasan_Daaboul • 0
0
votes
0
replies
105
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell communication ligand-receptor self-regulation
4 days ago by DGTool ▴ 20
1
vote
1
reply
186
views
geom_bar issue in ggplot2 with xlim()
geom_bar ggplot2 statistics R
updated 4 days ago by 82k • written 4 days ago by • 0
0
votes
2
replies
331
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix RNA-Seq Limma DESeq2 edgeR
4 days ago by Ezequiel • 0
2
votes
0
replies
193
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
5 days ago by micah ▴ 30
0
votes
0
replies
121
views
problems in installing rDock
rDock
updated 3 days ago by 44k • written 5 days ago by • 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq cellranger
updated 5 days ago by ▴ 30 • written 8 months ago by ▴ 870
1
vote
2
replies
731
views
Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 5 days ago by • 0 • written 2.6 years ago by • 0
1
vote
2
replies
386
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx cibersort error RNA-Seq deconvolution
updated 2 days ago by • 0 • written 3 months ago by ▴ 10
0
votes
0
replies
143
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 5 days ago by 162k • written 5 days ago by ▴ 30
0
votes
0
replies
154
views
Tera-scale metagenomic coassembly tool
co-assembly Metagenomics
5 days ago by Moinuddin • 0
0
votes
1
reply
195
views
Broad and Narrow peaks
ATAC ChIP seq
updated 5 days ago by 82k • written 5 days ago by ▴ 20
2
votes
1
reply
265
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 5 days ago by ★ 7.2k • written 6 days ago by • 0
0
votes
0
replies
154
views
How can i use ESM-1v ?
VEP ESM-1v
6 days ago by Meto • 0
0
votes
0
replies
162
views
Cell type annotation mixed with other type cells
cell annotation.
updated 6 days ago by 142k • written 6 days ago by • 0
2
votes
3
replies
350
views
Trimming tool
Trimming
updated 3 days ago by 44k • written 6 days ago by • 0
0
votes
0
replies
153
views
sci-RNA-seq
cell single seurat sci-rna-seq counts
6 days ago by kilcdincer ▴ 10
0
votes
2
replies
282
views
GG Sankey plot
GO sankey_plot gglpot
updated 6 days ago by 4.2k • written 6 days ago by • 0
0
votes
0
replies
172
views
genomic region of transcription factor
search HOMER motif
6 days ago by qudrat.nii ▴ 10
1
vote
5
replies
401
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 6 days ago by ★ 2.0k • written 7 days ago by • 0
0
votes
0
replies
161
views
Understanding behaviour of SCTransform in Seurat
Seurat scRNASeq normalization
updated 6 days ago by 142k • written 6 days ago by ▴ 90
4
votes
9
replies
655
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 3 days ago by ▴ 130 • written 8 days ago by ▴ 20
697 results • Page 3 of 14
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Answer: Conda, bioconda, anaconda, are they different?
Gene Set Enrichment Analysis
Comment: Unexpected read length from NGS
Answer: Unexpected read length from NGS
Answer: How I know if it is a batch effect or are real differences between my controls a
Answer: ¿How I know if it is a batch effect or are real differences between my controls
The Biostar Handbook. A bioinformatics e-book for beginners.
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Answer: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
Update: I ran CellBender on these samples and compared its results with SoupX and DecontX. vs SoupX: ![cellbender vs SoupX][1] …
Comment: Unexpected read length from NGS by QX • 0
thank you all!
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool by hashim.rana11 ▴ 20
Initially, I tried using Samtools and BCFtools, followed by running a script in Python (PyCharm) to measure nucleotide diversity![nucleoti…
Comment: Best Practice On Variant Discovery For Bacteria? by Ruqaiya • 0
I used HaploTypecaller but my plasmid reads are not present in the output vcf file ... but it's there in my input file
Answer: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool by Michael 54k
Variants should be called using a specialized mitochondrial variant caller, e.g.: [GATK Mutect2 CallMt][1] Then, pi, Tajima's D, and oth…
Comment: Splitting query fasta file for Diamond Blastp make the process faster? by kmat • 0
I used `seqkit split` to divide the query FASTA file into 10 parts and then ran `diamond blastp` on each file using 44 threads. The process…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI by zx8754 11k
Try: `--covar-name SEX,PARKISON` FID and IID are Family ID and Individual ID, they are not covariates. Side note, if PARKISON means "Par…
Comment: Error with BiocParallel. No barcodes files found by bio_info ▴ 10
I understand, thanks for explaining this to me. I'll take care of this in future.
Comment: How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tool by Pierre Lindenbaum 162k
> , but I was unsuccessful. what does it mean ?
Answer: Does prokka work the same on forward and reverse complementary reads? by igmin • 0
Prokka works the same on both forward and reverse complementary reads. It doesn't matter if your genetic sequences are in their original fo…
Comment: Construction of circos plot from WGS data by Anitha ▴ 10
Thank you for the information. But, I am still struggling like which data to use and how to process the input data to represent to build th…
Comment: Tools for chromosomal aneuploidy detection by cmdcolin ★ 3.8k
is there any reason why you do not like tools based on read depths?
Comment: CreateSeuratObject taking very long by eae6d2e7 • 0
Thank you for your reply! I followed your advice to convert to sparse matrix first but I got this error Error in Matrix::sparseMatrix(raw_…
Answer: Venter Genome Vcf by ericrkofman ▴ 20
I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from…
Comment: What is a good way to do gene differentials in single cell data where one group by ATpoint 82k
Preferred if you have true biological replicates. Can still be combined with my subsetting strategy, like use 100x different cells for the …
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