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1,000 results • Page 3 of 20
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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
7
replies
2.2k
views
About normalization of the datasets from Harmonized TCGA data
protein transcript normalisation
updated 11 weeks ago by 43k • written 21 months ago by ▴ 10
4
votes
7
replies
552
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 13 days ago by 43k • written 14 days ago by ▴ 20
4
votes
4
replies
847
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 10 months ago by 43k • written 10 months ago by • 0
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by 43k • written 24 days ago by • 0
4
votes
3
replies
588
views
Over Representation analysis altered pathways in common between comparisons plot
R Visualization DGE ORA
updated 6 months ago by ★ 2.0k • written 6 months ago by ▴ 10
4
votes
2
replies
627
views
Visualization package for Maf Files using Python
Python maftools Visualization MAF
updated 6 months ago by ★ 1.5k • written 6 months ago by ▴ 100
4
votes
9
replies
1.0k
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex illumina sequencing
updated 4 months ago by 141k • written 4 months ago by ▴ 120
4
votes
4
replies
480
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq Chip-Seq ATAC-Seq
8 weeks ago by qudrat.nii ▴ 10
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python Snakemake
5 months ago by Begonia_pavonina ▴ 150
4
votes
3
replies
753
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by stefano.iantorno ▴ 70
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
5
replies
2.0k
views
Whole blood single cell RNA-seq dataset?
RNA-Seq scRNA-Seq whole blood single cell
12 months ago by predeus ★ 1.9k
4
votes
6
replies
339
views
Protein loops
protein Loop
6 weeks ago by Curious ▴ 10
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by 141k • written 4 months ago by • 0
4
votes
11
replies
633
views
Remove X in row name with only number
GSVA
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 260
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
5
replies
779
views
Does adding reads cause batch effects?
kallisto RNAseq
10 months ago by bioinfo ▴ 150
4
votes
11
replies
1.6k
views
Check Strandedness
Check_Strandedness how_are_we_stranded_here leafcutter bash
updated 6 months ago by 20k • written 8 months ago by • 0
4
votes
6
replies
804
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
11 months ago by natalev ▴ 20
4
votes
16
replies
957
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
4
votes
16
replies
1.8k
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools RNAseq samtools BAM
updated 9 weeks ago by 43k • written 7 months 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 8 months ago by 22k
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by 43k • written 9.0 years ago by ▴ 10
4
votes
2
replies
561
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
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome .bed haplotypes HG38 coverage
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
4
replies
794
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 11 months ago by 21k • written 11 months ago by ▴ 20
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 11 weeks ago by ▴ 10 • written 3.4 years ago by ▴ 60
4
votes
4
replies
645
views
Feedback on mouse brain scRNA-seq quality control
mouse brain singe-cell scRNAseq quality-control
8 months ago by nshenoy ▴ 50
4
votes
5
replies
384
views
Filter out miRNA from ncRNA dataset
bowtie bowtie2 miRNA filtering ncRNA
updated 9 weeks ago by 82k • written 9 weeks ago by ▴ 10
4
votes
5
replies
1.4k
views
Distributed / parallel computing in bioinformatics
distributed-computing
updated 11 months ago by 43k • written 6.8 years ago by ▴ 750
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid software-error autogrid4
updated 11 months ago by 43k • written 3.1 years ago by • 0
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
2
replies
229
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 22 days ago by 161k • written 22 days ago by • 0
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis software
updated 11 months ago by 43k • written 6.2 years ago by • 0
4
votes
7
replies
563
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 24 days ago by ★ 3.8k • written 28 days ago by ▴ 140
4
votes
6
replies
2.4k
views
Why weblogo of biopython doesn't work?
Biopython Weblogo
updated 10 months ago by • 0 • written 20 months ago by ▴ 20
4
votes
6
replies
934
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by ★ 2.4k • written 11 months ago by • 0
4
votes
6
replies
836
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 24 days ago by 43k • written 4 months ago by ▴ 30
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 11 months ago by 82k • written 11 months ago by ▴ 160
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV WGS
updated 10 months ago by 43k • written 6.7 years ago by ▴ 40
4
votes
3
replies
689
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
5
replies
536
views
Which refseq_protein db to choose for zingiberaceae
local blastp blast
updated 8 months ago by 141k • written 8 months ago by • 0
4
votes
7
replies
798
views
Help with weighted nearest neighbor analysis
seurat single-cell
8 months ago by Chris ▴ 260
4
votes
7
replies
1.0k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by 4.5k • written 6 months ago by ▴ 20
4
votes
6
replies
1.8k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 9 months ago by 141k • written 9 months ago by • 0
4
votes
6
replies
633
views
Unexpected separation of RNA-seq samples on PCA plot
depletion PCA rRNA plot RNA-seq
5 months ago by Tihana ▴ 10
4
votes
3
replies
392
views
Single cell analysis of Cancer
cancer single-cell RNA-seq
updated 10 weeks ago by 141k • written 10 weeks ago by ▴ 20
4
votes
7
replies
764
views
Alternative for grep in a for loop
linux
updated 6 months ago by 43k • written 6 months ago by ▴ 20
4
votes
8
replies
607
views
GCP Snakemake
snakemake GCP
updated 3 months ago by 43k • written 3 months ago by ▴ 10
1,000 results • Page 3 of 20
Recent Votes
Comment: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
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Recent Replies
Answer: How to use limma to find differentially expressed genes in response to a continu by Gordon Smyth ★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J ▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing by cao510927 ▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Alex Reynolds 35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data by bk11 ★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq by GenoMax 141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq by dsull ★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Ram 43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i by ATpoint 82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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