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43
votes
6
replies
12k
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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
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
16
votes
11
replies
8.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
13 months ago by Ram 43k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 13 months ago by 43k • written 5.6 years ago by 16k
18
votes
40
replies
18k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 3.8 years ago by • 0 • written 7.8 years ago by ▴ 170
24
votes
4
replies
7.6k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 13 months ago by 43k • written 4.7 years ago by 82k
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 13 months ago by 43k • written 3.7 years ago by ▴ 340
26
votes
0
replies
2.4k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 13 months ago by 43k • written 4.5 years ago by 19k
10
votes
1
reply
2.3k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 13 months ago by 43k • written 4.1 years ago by ★ 2.5k
60
votes
52
replies
43k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 13 months ago by 43k • written 7.6 years ago by ★ 3.5k
13
votes
7
replies
6.2k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 13 months ago by 43k • written 3.6 years ago by 87k
21
votes
26
replies
9.6k
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
0
votes
0
replies
1.1k
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 13 months ago by 43k • written 3.6 years ago by 87k
12
votes
0
replies
2.7k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 13 months ago by 43k • written 3.7 years ago by 13k
1
vote
1
reply
1.4k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 13 months ago by 43k • written 3.7 years ago by • 0
4
votes
3
replies
4.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 13 months ago by 43k • written 6.0 years ago by ★ 4.0k
4
votes
1
reply
1.4k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 13 months ago by 43k • written 3.7 years ago by ▴ 40
3
votes
0
replies
3.6k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 13 months ago by 43k • written 3.8 years ago by 8.5k
20
votes
6
replies
5.6k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 13 months ago by 43k • written 7.6 years ago by ★ 5.2k
2
votes
2
replies
2.1k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 13 months ago by 43k • written 3.8 years ago by 3.2k
12
votes
5
replies
2.4k
views
Tutorial: FASTA file split
fasta
updated 13 months ago by 43k • written 3.9 years ago by 8.5k
0
votes
0
replies
1.8k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 13 months ago by 43k • written 3.9 years ago by ▴ 460
0
votes
0
replies
1.0k
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 13 months ago by 43k • written 3.9 years ago by ▴ 460
2
votes
1
reply
1.6k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 13 months ago by 43k • written 3.9 years ago by ★ 2.5k
73
votes
27
replies
28k
views
16 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by • 0 • written 10.2 years ago by 100k
59
votes
43
replies
21k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 13 months ago by 43k • written 6.6 years ago by ★ 1.4k
20
votes
7
replies
6.4k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 13 months ago by 43k • written 5.5 years ago by ▴ 800
4
votes
0
replies
1.8k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
nih tcga metadata cde
updated 13 months ago by 43k • written 4.1 years ago by 87k
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 6.4k
0
votes
0
replies
1.3k
views
Tutorial: Training GeneMark-EP+ ab-initio tool
abinitio training genemark annotation
updated 13 months ago by 43k • written 4.2 years ago by 8.5k
2
votes
1
reply
3.1k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 13 months ago by 43k • written 4.2 years ago by ▴ 10
5
votes
0
replies
3.3k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 13 months ago by 43k • written 4.2 years ago by ★ 3.5k
5
votes
2
replies
2.3k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 13 months ago by 43k • written 5.2 years ago by ▴ 10
50
votes
3
replies
4.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by 43k • written 5.3 years ago by 82k
21
votes
9
replies
6.5k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 14 months ago by 43k • written 10.9 years ago by 9.7k
287
votes
39
replies
183k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 13 months ago by 43k • written 9.7 years ago by 20k
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
34
votes
15
replies
6.5k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 13 months ago by 43k • written 4.8 years ago by ★ 9.4k
20
votes
4
replies
2.6k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 13 months ago by 43k • written 4.9 years ago by ▴ 180
15
votes
7
replies
6.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 13 months ago by 43k • written 7.9 years ago by ★ 3.5k
2
votes
0
replies
4.7k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 13 months ago by 43k • written 4.8 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 13 months ago by 43k • written 4.9 years ago by ★ 9.4k
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
10
votes
5
replies
23k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by 43k • written 5.8 years ago by ★ 9.4k
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Tutorial: Introduction to Gen3 Webinar
gen3 open-source data-commons big-data
updated 13 months ago by 43k • written 5.2 years ago by ▴ 310
0
votes
1
reply
1.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 13 months ago by 43k • written 6.2 years ago by ▴ 10
4
votes
2
replies
3.6k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 13 months ago by 43k • written 8.2 years ago by ★ 2.5k
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 13 months ago by 43k • written 5.3 years ago by 27k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.7 years ago by 9.7k
410 results • Page 4 of 9
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Answer: Seurat merge and batch correction
Answer: Seurat merge and batch correction
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
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Recent Replies
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t by yxwucq • 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error? by Mensur Dlakic ★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks? by HyperEvo • 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus by GenoMax 141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database by Art1ess • 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection by LauferVA 4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs by LauferVA 4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs by Pierre Lindenbaum 161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024 by geneontologyhelp ▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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