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42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
72
votes
48
replies
18k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 13 months ago by 43k • written 11.2 years ago by 33k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 11 months ago by 141k • written 10.4 years ago by 20k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 13 months ago by 43k • written 11.2 years ago by 6.0k
76
votes
14
replies
16k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
16
votes
7
replies
16k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 13 months ago by 43k • written 4.8 years ago by ▴ 310
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 12 months ago by 43k • written 7.8 years ago by 20k
77
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.5 years ago by 43k • written 9.9 years ago by 19k
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 5 weeks ago by ★ 1.2k • written 5.1 years ago by 16k
54
votes
5
replies
15k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 18 months ago by 43k • written 10.4 years ago by ★ 1.2k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
65
votes
15
replies
14k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 10 months ago by 43k • written 5.5 years ago by 16k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 13 months ago by 43k • written 7.5 years ago by ★ 4.7k
19
votes
3
replies
14k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 21 months ago by 43k • written 8.2 years ago by ★ 9.4k
12
votes
20
replies
14k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 13 months ago by 43k • written 4.9 years ago by ★ 16k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 13 months ago by 43k • written 11.1 years ago by 20k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 11 months ago by 43k • written 6.6 years ago by 87k
35
votes
13
replies
14k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 2.2 years ago by ★ 1.4k • written 2.5 years ago by 100k
64
votes
26
replies
14k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 13 months ago by 43k • written 6.6 years ago by 87k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 15 months ago by 43k • written 11.1 years ago by 100k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 2.2 years ago by 43k • written 9.4 years ago by ★ 2.4k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 13 months ago by 43k • written 9.4 years ago by ▴ 600
17
votes
0
replies
13k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 14 months ago by 43k • written 12.0 years ago by 11k
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 10 months ago by 43k • written 5.2 years ago by ▴ 170
45
votes
3
replies
13k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 12 months ago by 43k • written 8.0 years ago by ★ 3.2k
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 13 months ago by 43k • written 6.4 years ago by ▴ 800
32
votes
6
replies
12k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 13 months ago by 43k • written 3.9 years ago by 87k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 13 months ago by 43k • written 10.2 years ago by 6.0k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 21 months ago by 43k • written 8.2 years ago by ★ 1.8k
50
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 14 months ago by 43k • written 11.6 years ago by 100k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.9k
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.1 years ago by ▴ 410
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 21 days ago by 100k • written 8.1 years ago by 43k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 13 months ago by 43k • written 4.8 years ago by 6.3k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 2.0 years ago by 43k • written 10.0 years ago by ★ 1.8k
0
votes
0
replies
11k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
2.3 years ago by Wayne ★ 1.9k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 13 months ago by 43k • written 10.0 years ago by ▴ 810
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 months ago by • 0 • written 6.3 years ago by ▴ 320
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 13 months ago by 43k • written 10.0 years ago by ★ 1.8k
21
votes
13
replies
10k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 months ago by • 0 • written 22 months ago by 81k
18
votes
2
replies
10.0k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.1 years ago by 43k • written 9.5 years ago by ▴ 860
21
votes
26
replies
9.5k
views
11 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 5 weeks ago by ▴ 30 • written 4.4 years ago by 8.5k
14
votes
0
replies
9.5k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 12 months ago by 43k • written 7.6 years ago by ★ 3.9k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 13 months ago by 43k • written 10.7 years ago by 9.7k
10
votes
1
reply
9.2k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by 43k • written 6.6 years ago by ▴ 110
16
votes
5
replies
8.9k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 14 months ago by 43k • written 11.6 years ago by 20k
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 13 months ago by 43k • written 11.1 years ago by 100k
26
votes
15
replies
8.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 14 months ago by 43k • written 11.3 years ago by 9.7k
3
votes
2
replies
8.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.5k
3
votes
3
replies
8.7k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 11 months ago by 43k • written 6.3 years ago by ▴ 100
409 results • Page 2 of 9
Recent Votes
A: Out Of Disk Space With Picard Tools ?
Exporting WGCNA step-to-step network construction objects into igraph object
Comment: Downloaded pdb's on rcsb.org
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
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Commentator to GenoMax 141k
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Recent Replies
Comment: Per base sequence content failed miserably by GenoMax 141k
If this is 16S sequencing just follow the standard workflows like Qiime2.https://docs.qiime2.org/2024.2/tutorials/overview/
Comment: Out Of Disk Space With Picard Tools ? by kjngo • 0
Thanks changing the tmp dir fixed the out of disk space error for me as well.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies by shelkmike ★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou by nhaus ▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by bk11 ★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output by otieno43 ▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file by GenoMax 141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle by Ram 43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle by Joseph • 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
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