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328 results • Page 2 of 7
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Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed txt bed2txt sequencing Tutorial
8 months ago by opheevallee • 0
1
vote
2
replies
2.2k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy tool R Tutorial
updated 8 months ago by • 0 • written 3.0 years ago by ★ 3.8k
3
votes
1
reply
380
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools Tutorial Video Lesson
8 months ago by sdsubaru33 ▴ 30
65
votes
61
replies
15k
views
14 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000 genomes PLINK PCA Tutorial
8 months ago by Kevin Blighe 72k
70
votes
56
replies
16k
views
13 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
8 months ago by Kevin Blighe 72k
13
votes
0
replies
3.6k
views
Tutorial: Using R in Conda
R Tutorial
9 months ago by rohitsatyam102 ▴ 300
2
votes
0
replies
609
views
Tutorial: Sorting GFF/GTF files
annotation gff gtf sort Forum Tutorial
9 months ago by Juke34 ★ 5.3k
20
votes
6
replies
3.6k
views
Tutorial: Open Targets and programmatic access
drug API bioinformatics open targets disease Tutorial
9 months ago by Denise CS ★ 5.1k
2
votes
2
replies
426
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
SNP snpEff Annotation Tutorial chrMT
9 months ago by Arup Ghosh 2.8k
110
votes
115
replies
14k
views
18 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 10 months ago by ▴ 10 • written 2.5 years ago by 72k
10
votes
3
replies
593
views
Tutorial: FASTA file split
fasta split tutorial Tutorial
updated 10 months ago by 15k • written 10 months ago by ★ 5.3k
0
votes
0
replies
443
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
sequence BLAST databases Linux MacOSX Tutorial
10 months ago by brian.fristensky ▴ 160
0
votes
0
replies
317
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
sequence BLAST Data Science Covid19 Tutorial
10 months ago by brian.fristensky ▴ 160
2
votes
1
reply
513
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 COVID-19 viruses fastv Tutorial
10 months ago by chen ★ 2.1k
62
votes
25
replies
19k
views
12 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 11 months ago by 32k • written 7.2 years ago by 87k
51
votes
41
replies
14k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 11 months ago by • 0 • written 3.6 years ago by ★ 1.3k
180
votes
46
replies
62k
views
30 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 11 months ago by • 0 • written 8.6 years ago by 19k
19
votes
7
replies
3.9k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq R ggplot2 Tutorial
12 months ago by ahmad mousavi ▴ 520
4
votes
0
replies
652
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
tcga nih cde metadata Tutorial
12 months ago by Kevin Blighe 72k
10
votes
17
replies
1.6k
views
Tutorial: gene set filter/selection for training ab initio annotation tools
genome gene Tutorial
12 months ago by Juke34 ★ 5.3k
11
votes
1
reply
1.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
RNA-Seq scRNA-seq CITE-seq-count Tutorial
12 months ago by colindaven ★ 2.7k
9
votes
4
replies
3.2k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long reads minion oxford nanopore Tutorial
13 months ago by colindaven ★ 2.7k
0
votes
0
replies
420
views
Tutorial: Training GeneMark-EP+ ab-initio tool
annotation genemark training abinitio Tutorial
13 months ago by Juke34 ★ 5.3k
2
votes
1
reply
1.2k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
VCF Format SNP Filtering bcftools codes Tutorial
13 months ago by Asad Prodhan ▴ 10
5
votes
0
replies
1.2k
views
Tutorial: How to run CWL with Nextflow
nextflow cwl Tutorial
14 months ago by steve ★ 2.9k
129
votes
66
replies
30k
views
15 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
14 months ago by Kevin Blighe 72k
5
votes
2
replies
1.2k
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…
bedtools closest closestBed preRNA bedtools Tutorial
15 months ago by linuxborg2 ▴ 10
46
votes
3
replies
2.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
tutorial Tutorial how-to
15 months ago by ATpoint 48k
19
votes
9
replies
5.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl tutorial Tutorial
updated 15 months ago by ▴ 110 • written 7.8 years ago by 8.9k
250
votes
39
replies
124k
views
27 follow
Tutorial: How to download raw sequence data from GEO/SRA
GEO SRA fastq bam download Tutorial
updated 2 days ago by ▴ 70 • written 6.6 years ago by 19k
58
votes
26
replies
7.7k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
17 months ago by Kevin Blighe 72k
19
votes
15
replies
2.3k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
17 months ago by Shicheng Guo ★ 8.6k
18
votes
4
replies
1.5k
views
Tutorial: Bash One-liners collection on Github
bash-oneliners linux shell bioinformatics bash Tutorial
written 23 months ago by ▴ 160
42
votes
1
reply
31k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 18 months ago by 48k • written 9.0 years ago by ▴ 510
14
votes
7
replies
4.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq R HOMER peaks Tutorial
20 months ago by steve ★ 2.9k
2
votes
0
replies
2.0k
views
Tutorial: Calculation of TSS Scores for ATAC-seq Data
next-gen sequencing Tutorial
21 months ago by Sael ▴ 20
4
votes
1
reply
805
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0 Tutorial
updated 22 months ago by ▴ 120 • written 22 months ago by ★ 8.6k
11
votes
18
replies
5.7k
views
8 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
updated 22 months ago by ▴ 260 • written 22 months ago by 9.3k
0
votes
0
replies
444
views
Tutorial: Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT Tutorial
22 months ago by Shicheng Guo ★ 8.6k
16
votes
11
replies
11k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
cBioportal TCGA data_retrieval RNASeq R Tutorial
updated 22 months ago by ▴ 30 • written 4.5 years ago by ★ 4.3k
10
votes
5
replies
12k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup Tutorial
updated 2.1 years ago by ▴ 480 • written 2.7 years ago by ★ 8.6k
33
votes
15
replies
14k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
R TCGA GDC next-gen Tutorial
updated 2.1 years ago by ▴ 30 • written 4.5 years ago by ▴ 300
6
votes
3
replies
3.2k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
sequencing alignment rna-seq gene Tutorial
updated 2.1 years ago by ▴ 150 • written 2.5 years ago by ▴ 40
2
votes
11
replies
2.5k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf merge bcftools Tutorial
2.2 years ago by jaybee ▴ 80
0
votes
0
replies
592
views
Tutorial: Introduction to Gen3 Webinar
datacommons bigdata opensource gen3 Tutorial
2.2 years ago by Danielle ▴ 310
4
votes
2
replies
2.8k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
sequencing OpenGene Julia NGS Tutorial
updated 2.2 years ago by • 0 • written 5.2 years ago by ★ 2.1k
28
votes
4
replies
2.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics Tutorial
2.2 years ago by Jean-Karim Heriche 24k
59
votes
6
replies
8.1k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
2.3 years ago by Medhat 8.9k
5
votes
2
replies
1.4k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq tutorial Tutorial
2.4 years ago by saraoppenheim ▴ 50
5
votes
0
replies
923
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
structural variation dbvar Tutorial
updated 2.4 years ago by 48k • written 2.4 years ago by ▴ 50
328 results • Page 2 of 7
Recent Votes
Answer: How to combine 2 incomplete GTF
Answer: How to combine 2 incomplete GTF
A: Correct Way To Parse A Fasta File In Python
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
How to combine 2 incomplete GTF
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Recent Awards • All
Scholar to Nicolas Rosewick 9.3k
Scholar to Juke34 ★ 5.3k
Student to rafaelsolersanblas ▴ 70
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Recent Replies
Comment: how to select peaks at not transcribed genes by Lila M ▴ 910
rigth, it is a ChIP seq analysis
Comment: how to select peaks at not transcribed genes by ATpoint 48k
Which type data are we talking about? What was the experiment? There are literally no details in this question right now. It the assay meas…
Comment: How to combine 2 incomplete GTF by rafaelsolersanblas ▴ 70
Thank yo so much Juke!
Comment: MASURCA output by kilcdincer ▴ 10
Thank you. I understood ploidy part. My genome is supposed to belong to diploid Candida albicans. And genome size of diploid Candida alb…
Answer: How to combine 2 incomplete GTF by Juke34 ★ 5.3k
To give more precision to the @genomax comment: `agat_sp_compare_annotations.pl` will tell you the differences. Then you can choose to …
Comment: GSEA for RNA_seq dataset by ATpoint 48k
No problem. I am not really familiar with what the GSEA implementation from the Broad institute does. I personally use fgsea from Bioconduc…
Comment: How to combine 2 incomplete GTF by rafaelsolersanblas ▴ 70
Thank you!! I will try it :)
Comment: how to select peaks at not transcribed genes by Lila M ▴ 910
you mean in the call peaks? And what are those 232 not annotated peaks?aren't they tss associated to not transcribed genes?
Comment: How to combine 2 incomplete GTF by GenoMax 99k
Compare annotation tool `agat_sp_compare_annotations.pl` from [AGAT toolkit][1]. Install [**AGAT**][2] using `conda`. [1]: https://gith…
Comment: GSEA for RNA_seq dataset by 1961012 • 0
I am really sorry for asking for clarification because I am a beginner. I already used all genes (normalized and filtered) for GSEA using …
Comment: Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work by aka • 0
I work in a research laboratory that has specific demands that make the general pipeline not fit, I have to create it from scratch, but tha…
Comment: Extract chromosome 1 - 22 fasta file by shubhamkumbhar420 • 0
Thank you for your response! It worked !!!
Answer: How to combine 2 incomplete GTF by Michael Dondrup 48k
I made this perl script to compare two GFF files. It might be useful after some modifications (changing GFF version to 2?). Needs BioPerl i…
Comment: Snakemake with bwa_mem2_mem unable to open the ref file and doesn' t work by aka • 0
Hi, Thank you for your help! For the 1st it's a mistake sorry I change it and it's still the same. For the 2nd yes I am sure because wit…
Answer: R command worked yesterday, but stalls today? by ATpoint 48k
Make it simple and download that RDS file from command line with something like `wget`, this will give a status bar. Once downloaded just r…
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