Limit : this year
all time today this week this month this year
1,000 results • Page 5 of 20
Sort: Votes
Rank Views Votes Replies
3
votes
2
replies
325
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 6 weeks ago by 43k • written 11 weeks ago by ▴ 20
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST bowtie2 BWA alignment
9 months ago by cheesefish21 ▴ 10
3
votes
3
replies
517
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 6 months ago by ▴ 20 • written 6 months ago by ▴ 30
3
votes
6
replies
875
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq cells mRNA expression gene
updated 5 months ago by ★ 1.8k • written 5 months ago by ▴ 40
3
votes
5
replies
553
views
How to assess the quality of the assembly of unmapped reads ?
Pangenome Iterative-assembly
3 months ago by Sony ▴ 10
3
votes
7
replies
6.3k
views
running trimmomatic inside Trinity
Assembly Trinity RNA-seq trimmomatic
updated 10 months ago by 43k • written 8.1 years ago by ▴ 50
3
votes
19
replies
1.6k
views
Systematic errors at the end and beginning of reads in NGS panels
NGS error panels sequencing
updated 10 months ago by 10k • written 10 months ago by ▴ 20
3
votes
3
replies
361
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
6 weeks ago by Pumla • 0
3
votes
3
replies
508
views
How to proceed after Kraken2 analysis
rnaseq kraken
updated 6 months ago by ★ 2.0k • written 6 months ago by ★ 1.5k
3
votes
4
replies
828
views
Downstream analysis with DEseq2 normalization
DEseq2 integration
5 months ago by QX • 0
3
votes
9
replies
814
views
Understanding this analysis pipeline
reads
updated 10 months ago by 43k • written 10 months ago by • 0
3
votes
5
replies
344
views
Generating mpileup file using samtools
mpileup samtools
updated 14 days ago by 21k • written 14 days ago by • 0
3
votes
6
replies
833
views
Annotating genome based on Sequence
genome annotation
updated 6 months ago by 4.6k • written 6 months ago by ▴ 30
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 29 days ago by 43k • written 7.2 years ago by ▴ 310
3
votes
5
replies
3.2k
views
GO annotation for rice in an R package
annotation R
updated 3 months ago by • 0 • written 7.5 years ago by ▴ 10
3
votes
1
reply
434
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV WES
updated 8 months ago by 161k • written 8 months ago by ▴ 20
3
votes
6
replies
1.0k
views
Screen for transcription factors/genes that maybe the cause of a disease/difference in a phenotype
RNA-seq ATAC-seq
11 months ago by Chris ▴ 280
3
votes
7
replies
1.4k
views
VG Giraffe multi-mapped reads and definition for MAPQ score
vg
9 months ago by Hendricks27 • 0
3
votes
3
replies
823
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics qiime2 amplicon 16s dada2
updated 9 months ago by 3.6k • written 9 months ago by ▴ 720
3
votes
5
replies
814
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run DiffBind ChIP-seq
updated 5 months ago by ★ 2.0k • written 5 months ago by ▴ 10
3
votes
1
reply
392
views
GEO dataset Microarray data analysis help
R microarray NCBI GEO
updated 5 months ago by 43k • written 5 months ago by ▴ 20
3
votes
2
replies
415
views
t-test by row
R t-test
updated 5 months ago by ★ 2.0k • written 5 months ago by ▴ 20
3
votes
1
reply
589
views
PLINK .ped file issue
plink
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
5
replies
1.1k
views
I have a pair of read files where each is a mixed pool of reads from the Linked-read technology and Illumina short-read technology. Any suggestion on…
NGS clc-genomics illumina WGS
updated 7 months ago by 43k • written 7 months ago by ▴ 30
3
votes
26
replies
2.0k
views
6 follow
STAR Genome index Error
STAR
updated 7 months ago by 43k • written 7 months ago by • 0
3
votes
3
replies
269
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 4 days ago by 43k • written 18 days ago by • 0
3
votes
2
replies
743
views
Scvelo vs Monocle3
monocle3 scvelo
7 months ago by Chris ▴ 280
3
votes
3
replies
881
views
from fasta to gtf format?
gtf DE fasta
updated 4 months ago by ▴ 210 • written 3.1 years ago by ▴ 260
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 4 weeks ago by 43k • written 4.5 years ago by ▴ 10
3
votes
1
reply
440
views
How to BLAST a FASTA sequence with unknown organism source
chrZ BLAST FASTA
updated 7 months ago by 21k • written 7 months ago by • 0
3
votes
6
replies
879
views
Read multiple vcf files into R
R vcf
6 months ago by sousapaulo16 ▴ 20
3
votes
4
replies
696
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR volcano plotting R plot
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 270
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by ★ 4.3k • written 6.3 years ago by ▴ 980
3
votes
2
replies
284
views
Gene reads all zero for each sample
R salmon DE DESeq2
7 weeks ago by DYLAN NICO • 0
3
votes
5
replies
1.3k
views
Running purge_dups on a hybrid assembly (optical mapping + reads)
pacbio purge_dups Assembly bionano
updated 8 months ago by 6.4k • written 3.3 years ago by ▴ 300
3
votes
4
replies
670
views
Weighted analysis
RNA-seq
8 months ago by Peter • 0
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by 43k • written 5.5 years ago by • 0
3
votes
2
replies
4.8k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 9 months ago by ▴ 30 • written 4.5 years ago by ▴ 180
3
votes
4
replies
750
views
During alignment STAR has stopped at started alignment step
STAR
updated 8 months ago by 43k • written 9 months ago by • 0
3
votes
4
replies
368
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR MAGECK FACS
10 weeks ago by Aleksandr ▴ 10
3
votes
4
replies
321
views
Truncated metadata file report from ENA Portal API
ena python
7 days ago by Giulia • 0
3
votes
7
replies
522
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
10 weeks ago by Fadlilah ▴ 10
3
votes
7
replies
544
views
How does kallisto handle multi mapped reads?
kallisto
updated 12 weeks ago by ★ 6.0k • written 12 weeks ago by ▴ 150
3
votes
12
replies
602
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
6 weeks ago by Lila M ★ 1.2k
3
votes
2
replies
345
views
Illumina reads to be processed and prepared for reference genome alignment
genome alignment trimming next-gen Illumina
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 4 weeks ago by 43k • written 22 months ago by ▴ 20
3
votes
5
replies
1.6k
views
Uniprot API access to download .pdb files
PDB API Python Uniprot
11 months ago by BioGrad321 • 0
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
3
votes
6
replies
1.3k
views
Busco Folder: prfl
gene genome sequencing
updated 11 months ago by 43k • written 4.2 years ago by ▴ 20
3
votes
8
replies
656
views
Huge decrease of BUS records using bustools
single-cell bustools 10X
11 weeks ago by julien.wollbrett • 0
1,000 results • Page 5 of 20
Recent Votes
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
How can I perform Differential expression analysis with just one control and one cancer sample?
Comment: scRNAseq Differential expression analysis
Comment: scRNAseq Differential expression analysis
Comment: scRNAseq Differential expression analysis
Recent Locations • All
Chile, 8 minutes ago
India, 9 minutes ago
Japan, 23 minutes ago
Poland, 26 minutes ago
India, 33 minutes ago
United States, 36 minutes ago
Russia, 40 minutes ago
Recent Awards • All
Scholar to dsull ★ 6.0k
Popular Question to finswimmer 16k
Popular Question to Ezequiel • 0
Popular Question to alanh ▴ 170
Scholar to Peter 6.0k
Popular Question to ashkan ▴ 160
Supporter to Umer ▴ 50
Recent Replies
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Traffic: 1578 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6