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353 results • Page 3 of 8
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19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 27 days ago by 38k • written 9.8 years ago by 9.5k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 4 weeks ago by 38k • written 10.1 years ago by 97k
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
kraken k-mer database python Tutorial
5.0 years ago by Sej Modha 5.2k
18
votes
2
replies
9.5k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 12 months ago by 38k • written 8.4 years ago by ▴ 860
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 12 days ago by 38k • written 3.3 years ago by 7.7k
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by 38k • written 7.1 years ago by ★ 9.3k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 12 days ago by 38k • written 6.7 years ago by ▴ 160
17
votes
13
replies
1.7k
views
Tutorial: Screen shots of text (please don't)!
meta Forum Tutorial
6.0 years ago by Michael Dondrup 52k
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
12 days ago by Ram 38k
16
votes
5
replies
8.4k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 4 weeks ago by 38k • written 10.5 years ago by 20k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 12 days ago by 38k • written 3.8 years ago by ▴ 310
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 4 weeks ago by 38k • written 11.0 years ago by 9.9k
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 12 days ago by 38k • written 6.4 years ago by ★ 4.6k
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 270
15
votes
1
reply
6.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
BED SAM psl blast Tutorial
5.4 years ago by Joseph Hughes ★ 3.0k
15
votes
6
replies
5.7k
views
Tutorial: How to make your snakefiles self-documenting
snakemake Tutorial
updated 6.1 years ago by ★ 2.0k • written 6.4 years ago by ★ 1.7k
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 17 days ago by 38k • written 8.4 years ago by 11k
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
genvisr graphics bioconductor R Tutorial
updated 6.6 years ago by • 0 • written 6.8 years ago by 20k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 12 days ago by 38k • written 2.7 years ago by ▴ 300
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 17 days ago by 38k • written 5.3 years ago by ▴ 740
15
votes
1
reply
2.9k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
workshop training genomics lectures Tutorial
6.9 years ago by Malachi Griffith 19k
15
votes
3
replies
4.2k
views
Tutorial: NCBI blast tutorial
ncbi blast tutorial Tutorial
updated 6.9 years ago by ▴ 540 • written 6.9 years ago by 11k
15
votes
0
replies
6.3k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 4 weeks ago by 38k • written 10.8 years ago by 97k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
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
8.8k
views
Tutorial: How to generate PCA plot and heatmaps in R
RNA-Seq R PCA heatmap Tutorial
6.5 years ago by Ming Tommy Tang ★ 2.9k
14
votes
2
replies
6.1k
views
Tutorial: ChIP-seq analysis tutorial
Tutorials ChIP-Seq
updated 6 months ago by 38k • written 7.6 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
14
votes
2
replies
2.2k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R Tutorial
5.2 years ago by Jeremy Leipzig 21k
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
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
6
replies
5.2k
views
Tutorial: Trim & align paired-end reads in a single pass
trim align paired-end fastq pipe Tutorial
6.8 years ago by dariober 14k
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
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
11
replies
6.5k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI SRA Bioproject BioSample Tutorial
updated 5.7 years ago by ▴ 20 • written 6.0 years ago by ★ 2.4k
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
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
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
5
replies
7.6k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl Tutorial
6.5 years ago by Shicheng Guo ★ 9.3k
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
1
reply
2.0k
views
Tutorial: PCR Primer or Primer+Probe design
pcr probe rt-pcr qpcr primer
updated 21 months ago by ★ 14k • written 21 months ago by 84k
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
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
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
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
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
353 results • Page 3 of 8
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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Popular Question to sharmatina189059 ▴ 110
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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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