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353 results • Page 2 of 8
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45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 15 days ago by 38k • written 4.6 years ago by 84k
0
votes
0
replies
753
views
Tutorial: Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation bioimaging SLURM health
21 months ago by Erin Haskell | ELIXIR ▴ 470
1
vote
0
replies
965
views
Tutorial: Slurm and parallelization
slurm
21 months ago by Juke34 7.8k
1
vote
0
replies
938
views
Tutorial: How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo cytoscape
21 months ago by Pratik ▴ 880
12
votes
1
reply
2.0k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 22 months ago by ★ 14k • written 22 months ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 15 days ago by 38k • written 4.7 years ago by 70k
4
votes
0
replies
896
views
Tutorial: Long Read Genome Assembly Video Series
long-read genome-assembly
22 months ago by pbpanigrahi ▴ 420
0
votes
1
reply
752
views
Tutorial: Add Customized Filters in GDC
gdc
updated 22 months ago by 21k • written 22 months ago by ▴ 750
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 15 days ago by 38k • written 4.1 years ago by 16k
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 14 days ago by 38k • written 3.8 years ago by ★ 14k
4
votes
2
replies
2.0k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 14 days ago by 38k • written 3.8 years ago by ★ 9.3k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 14 days ago by 38k • written 2.7 years ago by ▴ 690
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 14 days ago by 38k • written 2.6 years ago by ▴ 140
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 14 days ago by 38k • written 6.6 years ago by 26k
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.8k
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 14 days ago by 38k • written 2.9 years ago by 84k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.4 years ago by ★ 7.7k
8
votes
0
replies
2.1k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
24 months ago by rpolicastro 11k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
6
votes
0
replies
1.5k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
24 months ago by rpolicastro 11k
8
votes
1
reply
1.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 14 days ago by 38k • written 2.0 years ago by 84k
20
votes
10
replies
4.7k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 14 days ago by 38k • written 2.6 years ago by 11k
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 14 days ago by 38k • written 2.0 years ago by 11k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 1.6k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 14 days ago by 38k • written 2.5 years ago by 2.9k
4
votes
0
replies
1.7k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 14 days ago by 38k • written 2.9 years ago by 70k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 14 days ago by 38k • written 3.8 years ago by ▴ 310
274
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 28 days ago by 38k • written 9.4 years ago by 20k
5
votes
0
replies
3.5k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 14 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
4.5k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 14 days ago by 38k • written 2.2 years ago by 127k
10
votes
0
replies
2.7k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 14 days ago by 38k • written 2.2 years ago by 127k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 14 days ago by 38k • written 2.2 years ago by ★ 23k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 22 days ago by 38k • written 9.0 years ago by ★ 1.9k
0
votes
1
reply
2.4k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 14 days ago by 38k • written 4.6 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 17 months ago by 38k • written 8.8 years ago by 19k
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 14 days ago by 38k • written 5.1 years ago by ▴ 340
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 26 days ago by 38k • written 9.2 years ago by 5.9k
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 12 days ago by • 0 • written 5.4 years ago by ▴ 130
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
14 days ago by Ram 38k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
14 days ago by Ram 38k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 days ago by 38k • written 4.6 years ago by 16k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 14 days ago by 38k • written 6.8 years ago by ▴ 160
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 14 days ago by 38k • written 3.6 years ago by 70k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 14 days ago by 38k • written 2.7 years ago by ▴ 300
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 14 days ago by 38k • written 3.5 years ago by 19k
10
votes
1
reply
2.0k
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 14 days ago by 38k • written 3.0 years ago by ★ 2.4k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 14 days ago by 38k • written 6.5 years ago by ★ 3.3k
10
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 14 days ago by 38k • written 2.5 years ago by 84k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 14 days ago by 38k • written 3.3 years ago by 7.8k
353 results • Page 2 of 8
Recent Votes
R Shiny Developer
Comment: Run nextflow sections sequentially
Comment: Nextflow rnaseq finishing early
A: hmmsearch vs hmmscan - e-value, speed, & output differences?
Answer: bash command to process a line
A: Forward And Reverse Strand Conventions
A: Forward And Reverse Strand Conventions
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Answer: Snakemake vs Nextflow Upcoming bioinformatics Project by cfos4698 ▴ 710
There are a lot of votes for Nextflow here, and it's generally pretty popular (and increasing in popularity). As a 'dissenting' voice, I'll…
Answer: Is it possible to use pseudoalignments.bam to run rMATs? by dsull ★ 4.0k
No, you can't do that with kallisto's bam files. For one, kallisto (by default) doesn't map to introns which is required by rMATs. You c…
Answer: genome annotation [sstart] [send] - how to get protein sequence from gene by shenwei356 8.0k
It means that the gene is on the negative/minus strand. So you need to compute the reverse complementary sequence before translating it to …
Answer: When to merge multiple fastq files into one for RNAseq analysis? by GenoMax 127k
As long as the sample name matches across the lanes they are pieces of the same sample. > I was thinking of combining the two fastq files…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
Yes, just put that fastq file (it'll be the same as any other kallisto bustools run, except you have just one fastq file and you have that …
Comment: Error building snpEff database "Transcript 'hypothetical_protein' already exist by Jane • 0
Hi, I have the same issue. After running the command, I run the "sh scripts/buildDbNcbi.sh U00096.2" to download again. Then the same issu…
Comment: bash command to process a line by saadleeshehreen ▴ 110
Thanks a lot. It worked
Answer: bash command to process a line by GenoMax 127k
With just one line example not sure if this will work awk -F '[|_]' '{print $2,$4}' your_file CU459141.1 CAM87240.1
Comment: RNA Sequencing and Vg pan -transcriptome build by kcarery • 0
Thank you! I found this as well and trying to understand it now.
Comment: RNA Sequencing and Vg pan -transcriptome build by kcarery • 0
Thank you so much! This is where I am leading back to as well! I don't have much insights into Hisat2. I am going to give it a go this week…
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by Juke34 7.8k
Interesting, why would you merge genes that are on different strands? They should be different genes. It cannot be done without modifying t…
Comment: featureCounts problem in reading Gff by Beatrice • 0
That's the output, so apparently I have the exon. Anyway, after running grep command the featureCounts worked, even though I didn't change …
Comment: bash command to process a line by saadleeshehreen ▴ 110
Yes the word start with lcl| and always sperated by _prot_. I am very naive pattern matching and extraction. I was trying to cut the field …
Comment: bash command to process a line by Mensur Dlakic ★ 23k
First, this is not bioinformatics. Simple pattern matching and extraction. Second, there isn't enough information in your message. Does ea…
Answer: How to find promoter sequence of a gene? by sunyeping ▴ 80
Steps to find transcriptional factors (TF) binding motifs 1. In NCBI gene, search and find the page for the gene of interest, using tool…
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