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232 results • Page 3 of 5
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14
votes
7
replies
5.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 12 days ago by 38k • written 6.9 years ago by ★ 3.3k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 12 days ago by 38k • written 2.5 years ago by 2.9k
14
votes
0
replies
7.9k
views
Tutorial: Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB ChIP-Seq Galaxy MACS RNA-Seq
updated 12 months ago by 38k • written 8.2 years ago by ▴ 860
13
votes
9
replies
4.0k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 9 months ago by ▴ 40 • written 15 months ago by ★ 1.1k
13
votes
3
replies
4.7k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 10 months ago by 38k • written 8.0 years ago by ▴ 860
13
votes
8
replies
3.1k
views
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
4 months ago by ATpoint 70k
12
votes
0
replies
2.0k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 12 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 12 days ago by 38k • written 2.0 years ago by 11k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 17 days ago by 38k • written 3.6 years ago by 7.7k
12
votes
5
replies
1.8k
views
Tutorial: FASTA file split
fasta
updated 12 days ago by 38k • written 2.8 years ago by 7.7k
12
votes
1
reply
4.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 12 days ago by 38k • written 3.0 years ago by 4.6k
12
votes
0
replies
7.3k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 11 months ago by 38k • written 8.2 years ago by ★ 4.6k
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 3 days ago by 38k • written 5.5 years ago by ▴ 570
12
votes
17
replies
2.2k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 3 months ago by 38k • written 7.8 years ago by 97k
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 12 days ago by 38k • written 3.8 years ago by ★ 14k
12
votes
1
reply
4.7k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 5 months ago by 38k • written 7.6 years ago by 3.5k
12
votes
4
replies
4.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 6 weeks ago by 38k • written 2.1 years ago by ▴ 120
11
votes
1
reply
2.3k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 6 months ago by ★ 1.8k • written 14 months ago by 14k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 12 days ago by 38k • written 2.2 years ago by ★ 23k
11
votes
6
replies
4.5k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 8 months ago by 38k • written 7.1 years ago by ★ 4.1k
10
votes
3
replies
4.1k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 9 weeks ago by 38k • written 8.5 years ago by ▴ 860
10
votes
7
replies
1.1k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 weeks ago by barslmn ★ 1.3k
10
votes
5
replies
18k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 12 days ago by 38k • written 4.7 years ago by ★ 9.3k
10
votes
7
replies
4.5k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 12 days ago by 38k • written 2.5 years ago by 84k
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 12 days ago by 38k • written 2.2 years ago by 127k
10
votes
2
replies
3.1k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 7 months ago by 38k • written 7.4 years ago by 20k
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 12 days ago by 38k • written 2.2 years ago by 127k
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 12 days ago by 38k • written 3.0 years ago by ★ 2.4k
9
votes
0
replies
8.1k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 5 weeks ago by 38k • written 11.0 years ago by ▴ 540
9
votes
0
replies
4.1k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 8 months ago by 38k • written 7.1 years ago by 19k
9
votes
0
replies
2.4k
views
Tutorial: Introduction to Next Generation Sequencing (Part 1)
polony emulsion-pcr next-gen-sequencing
updated 5 months ago by 38k • written 7.7 years ago by ▴ 90
9
votes
7
replies
6.0k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 6 months ago by • 0 • written 2.1 years ago by ▴ 240
9
votes
3
replies
3.9k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
9
votes
4
replies
9.0k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 12 days ago by 38k • written 3.7 years ago by 4.6k
8
votes
3
replies
2.5k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 8 months ago by 38k • written 7.1 years ago by 23k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 17 days ago by 38k • written 8.3 years ago by ▴ 580
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 20 days ago by 38k • written 8.9 years ago by ★ 1.8k
8
votes
17
replies
2.3k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 6 months ago by 38k • written 7.5 years ago by ▴ 340
8
votes
1
reply
1.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 12 days ago by 38k • written 2.0 years ago by 84k
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 23 days ago by 38k • written 9.0 years ago by ▴ 990
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 4 weeks ago by 38k • written 10.8 years ago by ▴ 120
7
votes
8
replies
3.0k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 3 months ago by 38k • written 7.7 years ago by ★ 2.1k
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 4 weeks ago by 38k • written 10.5 years ago by 11k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 8 months ago by 38k • written 7.1 years ago by ★ 1.8k
7
votes
14
replies
2.1k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 4 months ago by • 0 • written 13 months ago by ▴ 30
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 12 days ago by 38k • written 5.1 years ago by ▴ 340
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 4 weeks ago by 38k • written 10.7 years ago by 97k
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 11 days ago by 38k • written 4.4 years ago by ▴ 40
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 20 days ago by 38k • written 8.8 years ago by 7.7k
6
votes
2
replies
2.4k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 24 days ago by 38k • written 9.2 years ago by ▴ 610
232 results • Page 3 of 5
Recent Votes
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Recent Replies
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
Answer: how to know what adapter sequences to trim for RNA-seq? by Ming Tommy Tang ★ 2.9k
You may use fastp which detect adaptors by itself https://github.com/OpenGene/fastp#adapters
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