Limit : this year
all time today this week this month this year
1,000 results • Page 4 of 20
Sort: Votes
Rank Views Votes Replies
4
votes
6
replies
1.9k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 10 months ago by 142k • written 10 months ago by • 0
4
votes
2
replies
572
views
Can I still remove ambient RNA if I do not have raw barcode-gene matrix?
SoupX
6 months ago by malonzm1 ▴ 20
4
votes
7
replies
581
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 18 days ago by 43k • written 19 days ago by ▴ 20
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 12 months ago by 82k • written 12 months ago by ▴ 160
4
votes
7
replies
803
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 260
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers Enhancers
updated 3 months ago by ★ 16k • written 3 months ago by • 0
4
votes
5
replies
1.2k
views
STAR mapping - regarding output files content
STAR RNA-seq mapping
updated 8 months ago by ▴ 900 • written 8 months ago by • 0
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast remote databases Blastplus
updated 9 months ago by 142k • written 2.3 years ago by • 0
4
votes
5
replies
1.0k
views
VEP run with --af_gnomadg refuses to provide allele frequencies for extremely rare variants
vep gnomad
updated 8 months ago by ▴ 60 • written 9 months ago by 22k
4
votes
6
replies
813
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
11 months ago by natalev ▴ 20
4
votes
14
replies
2.7k
views
Is it possible to annotate single genes by snpeff
snp vcf
updated 10 months ago by 43k • written 6.7 years ago by ▴ 70
4
votes
3
replies
495
views
Parsing columns with awk
awk
updated 6 months ago by 43k • written 6 months ago by ▴ 300
4
votes
3
replies
761
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
8 months ago by stefano.iantorno ▴ 70
4
votes
1
reply
1.8k
views
How does FindNeighbors() and FindClusters() related and work?
seurat clustering
updated 8 months ago by ★ 2.4k • written 8 months ago by ▴ 120
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 5 weeks ago by 43k • written 5.5 years ago by ▴ 110
4
votes
3
replies
320
views
Getting less DE genes when incorporating all samples
RNA-seq differential-expression deseq2
updated 10 weeks ago by ★ 1.8k • written 11 weeks ago by ▴ 10
4
votes
5
replies
790
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
4
votes
1
reply
571
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler RNA-seq GSEA
updated 9 months ago by ★ 1.6k • written 9 months ago by ▴ 100
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan SNP
updated 10 months ago by 43k • written 9.5 years ago by • 0
4
votes
6
replies
1.1k
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
updated 6 months ago by ▴ 120 • written 7 months ago by ▴ 130
4
votes
3
replies
708
views
How to interpret output of PLINK association test (--assoc)
assoc
updated 8 months ago by 11k • written 8 months ago by ▴ 10
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core metaboigniter nextflow
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
4
votes
6
replies
347
views
Protein loops
protein Loop
6 weeks ago by Curious ▴ 10
4
votes
6
replies
848
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 29 days ago by 43k • written 5 months ago by ▴ 30
4
votes
5
replies
1.2k
views
tranfering sam file easy and fast way
SAM RNA-seq hisat2
updated 8 months ago by 43k • written 2.3 years ago by • 0
4
votes
4
replies
611
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by 142k • written 8 months ago by ★ 2.9k
3
votes
12
replies
963
views
why 99% reads failed to align in mir-seq analysis?
Fastqc bowtie1 miRNA-seq alignment differential-expression-analysis
3 months ago by mohammadhassanj ▴ 260
3
votes
5
replies
1.1k
views
kraken2 bacteria database 250GB+
metagenomics 16s kraken2 kraken
updated 5 months ago by 142k • written 5 months ago by ▴ 10
3
votes
4
replies
476
views
Discrepancy between the downloaded clinvar, dbNSFP and website
dbnsfp clinvar
updated 4 months ago by 43k • written 4 months ago by ▴ 40
3
votes
6
replies
1.1k
views
6 follow
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics nucleotide_diversity vcf
updated 11 weeks ago by ▴ 10 • written 5 months ago by ▴ 10
3
votes
4
replies
1.0k
views
R package DESeq2 in R 3.5.1
R
updated 11 months ago by 43k • written 16 months ago by ▴ 10
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 13 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
2
replies
309
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 26 days ago by 43k • written 8 weeks ago by ▴ 20
3
votes
4
replies
1.5k
views
fastPHASE -F provided to estimate haplotype frequencies, but no freqs in output
genomics phasing fastPHASE
updated 11 months ago by 43k • written 6.1 years ago by ▴ 10
3
votes
6
replies
1.3k
views
Busco Folder: prfl
gene genome sequencing
updated 10 months ago by 43k • written 4.2 years ago by ▴ 20
3
votes
2
replies
273
views
Gene reads all zero for each sample
R salmon DE DESeq2
4 weeks ago by DYLAN NICO • 0
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career bio
updated 11 months ago by 43k • written 6.2 years ago by ▴ 20
3
votes
3
replies
745
views
[bwa_aln_core] calculate SA coordinate... script.sh: line 91: 183402 Killed
HPC BWA Alignment
updated 11 months ago by 43k • written 2.3 years ago by ▴ 20
3
votes
3
replies
872
views
from fasta to gtf format?
gtf DE fasta
updated 3 months ago by ▴ 200 • written 3.0 years ago by ▴ 260
3
votes
5
replies
1.5k
views
Uniprot API access to download .pdb files
PDB API Python Uniprot
11 months ago by BioGrad321 • 0
3
votes
2
replies
276
views
Inject haplotypes into rGFA?
Pangenome
12 weeks ago by agd27 ▴ 130
3
votes
6
replies
836
views
Read multiple vcf files into R
R vcf
5 months ago by sousapaulo16 ▴ 20
3
votes
4
replies
778
views
Downstream analysis with DEseq2 normalization
DEseq2 integration
5 months ago by QX • 0
3
votes
1
reply
391
views
FastQC duplicates questions
FastQC RNA-seq
8 months ago by Beth ▴ 10
3
votes
19
replies
1.5k
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
4
replies
763
views
Should we update time periods in a Bibliometric analysis even after completing it, if it's found to be generating biased results due to recent study?
review bibliometric offtopic
9 weeks ago by Md. Al - Mustanjid ▴ 30
3
votes
3
replies
505
views
Need Control Gene Count Files
R RNA-Seq TCGA
updated 6 months ago by ▴ 20 • written 6 months ago by ▴ 30
3
votes
4
replies
383
views
What can cause broken read-pairs (chimeric read-pairs) in a sequencing run?
QC
12 weeks ago by William ★ 5.3k
3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam rna-seq
updated 6 months ago by 142k • written 6 months ago by ▴ 770
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
10 months ago by Chris ▴ 260
1,000 results • Page 4 of 20
Recent Votes
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
Decoy In Reference Assembly
Decoy In Reference Assembly
Comment: Bacterial plasmid analysis
Unsupervised clustering on gene expression data
Recent Locations • All
France, just now
United Kingdom, 1 minute ago
London, 1 minute ago
Armenia, 3 minutes ago
Netherlands, 3 minutes ago
Switzerland, 3 minutes ago
Japan, 5 minutes ago
Recent Awards • All
Popular Question to massa.kassa.sc3na ▴ 600
Teacher to shenwei356 8.5k
Popular Question to Apex92 ▴ 280
Popular Question to carlopecoraro2 ★ 2.5k
Popular Question to Jeol ▴ 20
Popular Question to lefthandgergo ▴ 10
Popular Question to mgranada3 ▴ 30
Recent Replies
Comment: Problem with data downloaded from Short Reads Archive (SRA) by GenoMax 142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples by ATpoint 82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA) by Begonia_pavonina ▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq by GenoMax 142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis by Daria ▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results by Bine ▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis by shenwei356 8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding by ATpoint 82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets by ATpoint 82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding by liorglic ★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis by Mensur Dlakic ★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file by rianna.collins • 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Traffic: 2419 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