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2
votes
13
replies
3.9k
views
pearson correlation between lncRNA and mRNA
pearson correlation R cor.test
updated 3.9 years ago by 45k • written 4.3 years ago by ▴ 40
4
votes
4
replies
2.2k
views
Generate QC report for STARsolo (html)
quality RNA-seq control STAR
updated 4.3 years ago by ★ 2.2k • written 4.3 years ago by ▴ 70
0
votes
4
replies
1.6k
views
gene expression databases
GEO high-throughput GEO2R
4.3 years ago by Zahra ▴ 110
0
votes
0
replies
901
views
Salmon Library Types
salmon RNA-Seq
4.3 years ago by aka ▴ 10
0
votes
7
replies
4.0k
views
Issues with genome indexing with bowtie2-build
bowtie2
updated 4.3 years ago by ▴ 80 • written 4.3 years ago by • 0
1
vote
1
reply
1.4k
views
Install STAR-Fusion inside Conda (Snakemake) fails
snakemake STAR-Fusion Conda
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
3
votes
6
replies
2.4k
views
VEP chromosome name query
ensembl VCF annotation VEP
4.3 years ago by prasundutta87 ▴ 730
0
votes
5
replies
1.5k
views
AnalysingTopHat and Fast QC results
tophat FastQC RNA-seq
updated 2.6 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.5k
views
RNAseq analysis using EdgeR or Deseq2 for generating fold change graph
change fold RNAseq
4.3 years ago by najibveto ▴ 130
0
votes
0
replies
1.5k
views
Detect fusion genes from WES data
Fusion fusion WES genes
20 months ago by enes ▴ 40
2
votes
2
replies
1.6k
views
Should I subset my data before running EstimateDisp() in RNA-seq analysis ?
RNAseq edgeR EstimateDisp
4.3 years ago by Basti ★ 2.1k
5
votes
2
replies
1.2k
views
Annotation Mycoplasma genome using Prokka
Mycoplasma Annotation Prokka
4.3 years ago by A_heath ▴ 170
0
votes
3
replies
1.6k
views
Extract specific gene id from an annotation file
R RNA-seq Linux
updated 4.3 years ago by ▴ 940 • written 4.3 years ago by ▴ 30
3
votes
12
replies
3.8k
views
Amount of unique variants in VCF with linux terminal
variants unique VCF linux
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 10
3
votes
4
replies
1.4k
views
How to create boxplot with jitter points where one point is labelled
Boxplot script Labell Jitter R
4.3 years ago by Roland • 0
1
vote
3
replies
1.6k
views
Filtering duplicates with MACS2 after re-sequencing a sample to increase read depth
macs2 chip-seq
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
2
votes
5
replies
2.2k
views
UMAP and "equal" objects
visualization
updated 4.3 years ago by • 0 • written 4.3 years ago by ★ 3.0k
0
votes
2
replies
1.5k
views
Is the pileup value the ATAC-seq counts?
ATAC
4.3 years ago by cthangav ▴ 110
0
votes
0
replies
418
views
Mitochondrial localization signal for CRISPR/CAS
CRISPRcas
4.3 years ago by chiti.agarwal ▴ 10
1
vote
0
replies
712
views
Pattern Search function in MicrobiomeAnalyst
MicrobiomeAnalyst metagenomics
4.3 years ago by GlycineMax ▴ 10
3
votes
4
replies
4.2k
views
Which R function can be used for intersection of genomic coordinates from one file and check if the coordinates are within a specific range?
coordinates R Genomic
4.2 years ago by bioinfo89 ▴ 60
1
vote
2
replies
798
views
FASTQC per base sequence quality
FASTQC
4.3 years ago by BIN • 0
0
votes
0
replies
767
views
Intersecting multiple bed files with reporting the number of base pairs of overlap between the features - Pybedtools
Pybedtools Coordinates Python Bedtools
4.3 years ago by BioICoder ▴ 40
0
votes
2
replies
984
views
De Novo Assembly from Oligos
assembly denovo
updated 4.3 years ago by ★ 1.5k • written 4.3 years ago by • 0
1
vote
3
replies
2.1k
views
Job: Bioinformaticist or computational biologist opportunity at Pattern Ag (CA, USA) in metagenomics
metagenomics python development NGS
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.2k
views
For Loop for .fa files in folder
windows BLAST
updated 2.3 years ago by 45k • written 4.3 years ago by • 0
2
votes
2
replies
1.4k
views
Gene Regulatory Networks on Single Cell RNAseq Datasets
GRN Transcription scRNAseq ChIPseq Factors
4.3 years ago by fouerghi20 ▴ 90
1
vote
2
replies
1.1k
views
Blast Database on External Hard Disk
Standalone NCBI BLAST Local
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
4
votes
12
replies
6.7k
views
How to Speed Up BLASTp
blastp linux-cluster BLAST nr-database
updated 4.3 years ago by ★ 30k • written 4.3 years ago by • 0
0
votes
0
replies
3.3k
views
2: Position guide is perpendicular to the intended axis. Did you mean to specify a different guide `position`?
EnhancedVolcano
4.3 years ago by Eko • 0
0
votes
5
replies
1.4k
views
how can i find expressions of miRNAs using TCGA
mirna tcga
updated 3.7 years ago by 154k • written 4.3 years ago by ▴ 10
1
vote
3
replies
1.4k
views
Demultiplexing reads from three libraries (non, single and dual indices)
demultiplexing bcl2fastq Illumina
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
1
vote
1
reply
778
views
What is the most convenient way to interact with ncbi?
databases nsbi
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 50
0
votes
0
replies
844
views
News: Webinar on BRENDA database - comprehensive enzyme information system
enzyme protein database
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 470
3
votes
4
replies
1.5k
views
Mapping reads to a very small reference
bowtie2 mapping
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by • 0
0
votes
2
replies
1.6k
views
Exclude non shared SNPs from two datasets with PLINK
Human SNPs Genome Shared PLINK Sites
4.3 years ago by GIACOMO FRANCESCO • 0
0
votes
1
reply
816
views
How to find conserved enhancers between human cell lines?
chip enhancer h3k27ac
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 10
6
votes
2
replies
930
views
Differentially expressed genes and their promoter region accessiblity
gene regulation
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 20
1
vote
0
replies
538
views
plink vs MBMDR results :
Epistasis MBMDR plink
4.3 years ago by Mollie ▴ 10
4
votes
22
replies
11k
views
samtools coverage usage
NGS
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 20
0
votes
0
replies
725
views
How to calculate RMSD and binding energy from the already docked ligand-receptor
python protein docking pdb structure
4.3 years ago by gundalav ▴ 380
0
votes
0
replies
647
views
Create a genomic portal web app
cbioportal genome shinyapp web server
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
1
vote
8
replies
3.2k
views
Protein Structure drawing on graph paper
Protein
updated 2.8 years ago by 45k • written 4.3 years ago by ▴ 140
5
votes
3
replies
2.3k
views
Download multiple SRA samples and convert into fasta format at once
fasta SRA fastq-dump prefetch
4.3 years ago by twangxxx • 0
7
votes
4
replies
1.8k
views
Should I remove an overrepresented sequence from one Fastq file from my RNA Seq data?
fastqc overrepresented RNA-Seq sequences
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by • 0
2
votes
5
replies
1.8k
views
Is it appropriate to resize peak before ATAC/ChIP-Seq differential peak analysis
ATAC
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 30
1
vote
2
replies
928
views
is there a proper way to choose clusters in hierarchical clustering?
Hierarchical-clustering dendogram R
updated 4.3 years ago by 3.3k • written 4.3 years ago by ▴ 140
0
votes
0
replies
544
views
microanalysis of zebrafish genome
genomics
4.3 years ago by aranyak111 • 0
0
votes
1
reply
1.5k
views
CNVkit methods and parameters
WGS CNV analysis
updated 4.3 years ago by ▴ 60 • written 4.3 years ago by ▴ 20
0
votes
0
replies
799
views
cnvkit genemetrics --ttest
ffpe oncology cnv cnvkit cna
updated 4.3 years ago by 9.8k • written 4.3 years ago by ▴ 60
121,990 results • Page 629 of 2440
Recent Votes
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: TMM-Normalization
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
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Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Answer: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
This question is about simulating reads and not read mapping.
Comment: GUI commercial software for 10x single cell gene expression analysis by yura.grabovska ▴ 830
I have fun memories of month-long discussions with Illumina support about their GenomeStudio methylation module asking them to provide info…
Comment: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by Arup Ghosh 3.4k
Try the references from the following publications. https://www.nature.com/articles/s41591-024-03150-z https://www.science.org/doi/10.112…
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
There's an easier way than manually renaming the output files (though you can do this, and it works) - you can use the `name` (aka `stageAs…
Answer: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 i by ecSeq Bioinformatics ▴ 20
Last Call for this event. Apply now, if you like to join.
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
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