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Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 7 months ago by 40k • written 10.7 years ago by 6.0k
7
votes
14
replies
3.0k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
20
votes
14
replies
3.6k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 5 months ago by 40k • written 7.4 years ago by ▴ 460
50
votes
14
replies
75k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 11 months ago by 40k • written 9.9 years ago by ★ 1.2k
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 23 months ago by 40k • written 9.3 years ago by 19k
19
votes
13
replies
6.8k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 1 day ago by 14k • written 15 months ago by 77k
4
votes
13
replies
11k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 3 months ago by 40k • written 4.6 years ago by ▴ 140
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 19 months ago by 40k • written 8.9 years ago by ★ 2.4k
28
votes
13
replies
11k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 20 months ago by ★ 1.3k • written 23 months ago by 98k
17
votes
13
replies
1.9k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 4 months ago by 40k • written 6.5 years ago by 53k
8
votes
12
replies
6.4k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 5 months ago by 40k • written 7.3 years ago by 13k
31
votes
12
replies
28k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 7 months ago by 40k • written 10.0 years ago by 98k
12
votes
11
replies
7.0k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 4 months ago by 40k • written 6.6 years ago by ★ 2.4k
6
votes
11
replies
5.2k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 7 months ago by 40k • written 6.8 years ago by ▴ 50
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 6 months ago by 40k • written 6.9 years ago by ★ 4.7k
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
27
votes
10
replies
70k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
21
votes
10
replies
6.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 6 months ago by 40k • written 3.1 years ago by 12k
6
votes
10
replies
4.8k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 6 months ago by 40k • written 5.6 years ago by ▴ 370
16
votes
9
replies
5.8k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 15 months ago by ▴ 70 • written 22 months ago by ★ 1.2k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.9k
9
votes
9
replies
3.9k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 4 months ago by 40k • written 6.0 years ago by 86k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 7 months ago by 40k • written 10.3 years ago by 9.7k
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 6 months ago by 40k • written 9.5 years ago by ★ 1.8k
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 months ago by 40k • written 10.3 years ago by ★ 3.0k
7
votes
8
replies
3.2k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 9 months ago by 40k • written 8.2 years ago by ★ 2.2k
31
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 6 months ago by 40k • written 9.5 years ago by ▴ 810
81
votes
8
replies
8.2k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 6 months ago by 40k • written 9.3 years ago by 19k
23
votes
8
replies
5.1k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 21 months ago by 40k • written 9.1 years ago by 24k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 5 months ago by 40k • written 7.6 years ago by ★ 1.1k
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 4 months ago by 40k • written 6.1 years ago by 86k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
20
votes
7
replies
6.0k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 6 months ago by 40k • written 5.0 years ago by ▴ 760
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 weeks ago by 77k • written 3.5 years ago by 5.5k
14
votes
7
replies
5.9k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 6 months ago by 40k • written 7.4 years ago by ★ 3.3k
11
votes
7
replies
9.2k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 4 months ago by 40k • written 2.6 years ago by ▴ 360
8
votes
7
replies
8.0k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 20 months ago by 40k • written 9.8 years ago by ★ 2.6k
12
votes
7
replies
5.4k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 6 months ago by 40k • written 3.0 years ago by 86k
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
6 months ago by barslmn ★ 1.8k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 7 months ago by 40k • written 9.7 years ago by 6.0k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 7 months ago by 40k • written 11.1 years ago by 98k
43
votes
6
replies
22k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 20 months ago by ▴ 40 • written 2.5 years ago by 12k
11
votes
6
replies
4.7k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 14 months ago by 40k • written 7.6 years ago by ★ 4.2k
13
votes
6
replies
5.6k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 5 months ago by 40k • written 7.3 years ago by 14k
379 results • Page 2 of 8
Recent Votes
A: .gstmp extension on .bam files downloaded from google bucket; and EOF marker is
Comment: Significance testing of top vs. random SNPs
Answer: Search RCSB with a list of protein names?
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
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Comment: bedtools intersect by position & stand not working even with common regions by rfran010 ▴ 830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files by rfran010 ▴ 830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly. If it's not done alre…
Answer: vcf.gz to vcf by Mark ★ 1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names? by Jiyao Wang ▴ 340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow? by Mark ★ 1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'. Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again... by GenoMax 134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files by Alex Reynolds 35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space: ``` bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
```bash # Obtain the makefile curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile # Run the makefile make vcf ``` Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook by Tully • 0
> System Information: Ubuntu 22.04 (WSL2) > > Shell: zsh > > Installation Verification: Yes, doctor.py OK [1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File by Reem • 0
Did it affect the bamtofastq output file? if so how did you solve the problem? Thanks
Answer: How to import bigwig files into igvR by Trivas ★ 1.5k
You could try seeing if this fixes your issue with rtracklayer: https://support.bioconductor.org/p/p133244/
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
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