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358 results • Page 2 of 8
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72
votes
48
replies
16k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 3 months ago by 39k • written 10.3 years ago by 33k
34
votes
17
replies
15k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 5 weeks ago by 130k • written 9.6 years ago by 20k
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 3 months ago by 39k • written 10.3 years ago by 5.9k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 20 months ago by 39k • written 9.0 years ago by 19k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 4 months ago by 39k • written 10.1 years ago by 9.6k
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 8 months ago by 39k • written 9.5 years ago by ★ 1.2k
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 9 weeks ago by 39k • written 7.0 years ago by 20k
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 12 weeks ago by 39k • written 6.6 years ago by ★ 4.6k
11
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 23 days ago by 39k • written 5.7 years ago by 85k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 3 months ago by 39k • written 10.2 years ago by 20k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 12 weeks ago by 39k • written 4.0 years ago by ▴ 310
63
votes
13
replies
12k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 16 months ago by 39k • written 8.6 years ago by ★ 2.3k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 4 months ago by 39k • written 10.3 years ago by 98k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 3 months ago by 39k • written 8.6 years ago by ▴ 580
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 3 months ago by 39k • written 11.2 years ago by 9.9k
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 9 weeks ago by 39k • written 7.2 years ago by ★ 3.2k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 14 days ago by 39k • written 4.7 years ago by 16k
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 12 weeks ago by 39k • written 4.0 years ago by ★ 14k
18
votes
3
replies
12k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 10 months ago by 39k • written 7.3 years ago by ★ 9.3k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 12 weeks ago by 39k • written 5.7 years ago by 85k
65
votes
26
replies
12k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 12 weeks ago by 39k • written 4.3 years ago by 16k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 3 months ago by 39k • written 9.4 years ago by 5.9k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 3 months ago by 39k • written 5.5 years ago by ▴ 750
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 10 months ago by 39k • written 7.3 years ago by ★ 1.8k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 3 months ago by 39k • written 9.2 years ago by ★ 1.9k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 14 months ago by 39k • written 9.2 years ago by ★ 1.8k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 3 months ago by 39k • written 9.2 years ago by ▴ 800
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 3 months ago by 39k • written 9.2 years ago by ★ 1.8k
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 3 months ago by 39k • written 2.7 years ago by 2.9k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 3 months ago by 39k • written 4.3 years ago by ▴ 140
18
votes
2
replies
9.6k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 14 months ago by 39k • written 8.6 years ago by ▴ 860
31
votes
6
replies
9.5k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 12 weeks ago by 39k • written 3.1 years ago by 85k
0
votes
0
replies
9.5k
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
17 months ago by Wayne ★ 1.8k
10
votes
4
replies
9.5k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 12 weeks ago by 39k • written 3.9 years ago by 4.9k
60
votes
6
replies
9.0k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by 39k • written 9.8 years ago by 9.6k
14
votes
0
replies
9.0k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.9k
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 21 days ago by 39k • written 5.4 years ago by ▴ 310
19
votes
4
replies
8.5k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 3 months ago by 39k • written 10.3 years ago by 98k
16
votes
5
replies
8.5k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 3 months ago by 39k • written 10.7 years ago by 20k
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
27
votes
13
replies
8.3k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 16 months ago by ★ 1.2k • written 20 months ago by 98k
9
votes
0
replies
8.2k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
20
votes
4
replies
8.2k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 4.2k
24
votes
15
replies
8.1k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 3 months ago by 39k • written 10.4 years ago by 9.6k
14
votes
0
replies
8.0k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 14 months ago by 39k • written 8.4 years ago by ▴ 860
81
votes
8
replies
8.0k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 3 months ago by 39k • written 9.0 years ago by 19k
3
votes
3
replies
8.0k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 21 days ago by 39k • written 5.5 years ago by ▴ 100
2
votes
2
replies
7.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 22 days ago by 39k • written 5.5 years ago by ★ 2.4k
8
votes
7
replies
7.8k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 16 months ago by 39k • written 9.5 years ago by ★ 2.6k
358 results • Page 2 of 8
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Comment: conda: command not found: gatk. by bestone ▴ 10
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk. by bestone ▴ 10
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left). https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem by Pierre Lindenbaum 155k
the HD header is not generated by bwa, but you can add it using awk: bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity by Kiran ▴ 80
Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem by GokalpC ▴ 80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort. ANGSD…
Comment: Mapping a predicted sequence to a genome by Mensur Dlakic ★ 23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome by Andy • 0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome by Mensur Dlakic ★ 23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
Comment: How to get information about promoter from bulk-RNAseq? by rfran010 ▴ 170
I'll just add what I did with my own dataset of ribo depleted RNA-seq: I took predicted enhancer-promoter interaction datasets from UCSC a…
Answer: How to get information about promoter from bulk-RNAseq? by rfran010 ▴ 170
What type of RNA-seq data do you have? With polyA, I think it will be hard to incorporate enhancer info without additional datasets. …
Comment: Reorder GO terms using R by hellokwmin • 0
Thank you so much. It worked perfectly.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
Thank you so much, Gordon!
Comment: Help with running ATAC using Encode pipeline by rfran010 ▴ 170
Yes, it is a lot to take in. In your input json, is "atac.fastqs_wt_rep2_R2" valid? This key should match exactly what is given in the exa…
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