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Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 14 months ago by 43k • written 12.1 years ago by ▴ 540
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 5.3 years ago by ▴ 10
3
votes
2
replies
2.7k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 11 months ago by 43k • written 7.1 years ago by ▴ 650
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
4
votes
2
replies
7.2k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 14 months ago by 43k • written 12.0 years ago by 100k
7
votes
2
replies
3.9k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 13 months ago by 43k • written 8.1 years ago by ▴ 850
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 18 months ago by ▴ 830 • written 2.6 years ago by ▴ 310
6
votes
2
replies
2.7k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 14 months ago by 43k • written 10.3 years ago by ▴ 610
7
votes
2
replies
12k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 21 months ago by 43k • written 8.2 years ago by ★ 1.8k
15
votes
2
replies
3.0k
views
Tutorial: Introduction to bedtools.
bedtools
updated 14 months ago by 43k • written 9.5 years ago by 12k
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
3
votes
2
replies
8.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.5k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 months ago by Ming Tommy Tang ★ 3.9k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.1k
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 43k • written 7.6 years ago by ★ 3.9k
7
votes
2
replies
1.9k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.7 years ago by ▴ 90
23
votes
2
replies
5.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 20 months ago by ▴ 40 • written 3.0 years ago by 8.6k
22
votes
2
replies
6.0k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 12 months ago by 43k • written 7.5 years ago by ★ 2.1k
0
votes
2
replies
5.4k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.5 years ago by 43k • written 9.8 years ago by 9.7k
0
votes
2
replies
2.4k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 13 months ago by 43k • written 7.7 years ago by ▴ 190
10
votes
2
replies
3.5k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 21 months ago by 43k • written 8.5 years ago by 20k
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 11 months ago by 43k • written 6.4 years ago by ★ 3.4k
5
votes
2
replies
3.1k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 11 months ago by 43k • written 7.1 years ago by ★ 9.4k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
0
votes
1
reply
1.1k
views
Tutorial: Add Customized Filters in GDC
gdc
updated 2.9 years ago by 21k • written 2.9 years ago by ★ 1.2k
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
1
vote
1
reply
1.8k
views
Tutorial: Live webinar: Implications of Next Generation Sequencing in Molecular Diagnosis of Cancer on 28 Sep 2016
alignment sequencing genome SNP
updated 13 months ago by 43k • written 7.7 years ago by ▴ 70
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 14 months ago by 43k • written 12.0 years ago by 100k
22
votes
1
reply
3.2k
views
Tutorial: Introduction To R Course Materials Available
R
updated 16 months ago by 43k • written 12.0 years ago by 26k
2
votes
1
reply
3.2k
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
2
votes
1
reply
426
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 3 months ago by 43k • written 3 months ago by ▴ 120
50
votes
1
reply
8.8k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 14 months ago by 43k • written 3.6 years ago by 82k
5
votes
1
reply
4.2k
views
Tutorial: Mini-tutorial: How to fix too-long sequence names in SyMAP
alignment
updated 16 months ago by 43k • written 8.9 years ago by 8.4k
3
votes
1
reply
3.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 12 weeks ago by ▴ 120 • written 2.8 years ago by 87k
6
votes
1
reply
448
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
1
reply
61k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 21 months ago by 4.2k • written 21 months ago by ▴ 20
15
votes
1
reply
3.2k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 13 months ago by 43k • written 8.0 years ago by 19k
0
votes
1
reply
550
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
6
votes
1
reply
3.0k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 14 months ago by 43k • written 10.0 years ago by ▴ 220
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 11 months ago by 43k • written 6.5 years ago by ★ 1.7k
3
votes
1
reply
3.8k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
4
votes
1
reply
6.1k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 14 months ago by 43k • written 12.0 years ago by ▴ 360
3
votes
1
reply
1.7k
views
Tutorial: Various youtube tutorials, including using proteomicsdb, finding adaptors, etc.
RNA Python
updated 13 months ago by 43k • written 8.1 years ago by ★ 1.1k
12
votes
1
reply
5.1k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 18 months ago by 43k • written 8.7 years ago by 3.5k
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by 43k • written 6.7 years ago by ▴ 110
2
votes
1
reply
2.7k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 15 months ago by 161k • written 15 months ago by ★ 2.1k
0
votes
1
reply
2.7k
views
Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
2
votes
1
reply
3.0k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 19 months ago by 43k • written 8.7 years ago by ★ 1.1k
411 results • Page 5 of 9
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Popular Question to SHN ▴ 40
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Recent Replies
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
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Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ by GenoMax 142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file? by bk11 ★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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