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357 results • Page 3 of 8
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10
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1
reply
7.7k
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Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 19 days ago by 39k • written 5.7 years ago by ▴ 110
12
votes
5
replies
7.7k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 weeks ago by 39k • written 7.0 years ago by ★ 9.3k
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 17 days ago by 39k • written 5.4 years ago by ▴ 10
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 3 months ago by 39k • written 11.1 years ago by 98k
18
votes
22
replies
7.5k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by 39k • written 3.5 years ago by 7.9k
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
11 weeks ago by Ram 39k
11
votes
2
replies
7.4k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 24 days ago by 39k • written 6.2 years ago by ★ 1.5k
12
votes
0
replies
7.4k
views
Tutorial: Plot average methylation levels across TSS region
bedtools RRBS R methylation
updated 14 months ago by 39k • written 8.3 years ago by ★ 4.6k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
17 days ago by Ram 39k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 16 days ago by 39k • written 2.3 years ago by ▴ 300
42
votes
19
replies
7.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by 39k • written 10.3 years ago by 4.1k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 18 days ago by 39k • written 5.5 years ago by ★ 3.4k
6
votes
4
replies
7.0k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 3 months ago by 39k • written 10.2 years ago by 11k
60
votes
2
replies
7.0k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
4
votes
2
replies
6.9k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 3 months ago by 39k • written 11.0 years ago by 98k
64
votes
5
replies
6.8k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 months ago by 39k • written 7.8 years ago by 12k
26
votes
17
replies
6.8k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 8 months ago by 39k • written 8.8 years ago by 5.9k
12
votes
11
replies
6.7k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 25 days ago by 39k • written 6.2 years ago by ★ 2.4k
32
votes
4
replies
6.6k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 11 weeks ago by 39k • written 4.6 years ago by ★ 1.5k
49
votes
1
reply
6.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 3 months ago by 39k • written 2.7 years ago by 72k
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 3 months ago by 39k • written 10.8 years ago by 98k
2
votes
0
replies
6.5k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 17 days ago by 39k • written 5.5 years ago by ▴ 310
23
votes
4
replies
6.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 11 weeks ago by 39k • written 3.8 years ago by 72k
15
votes
1
reply
6.4k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 18 days ago by 39k • written 5.6 years ago by ★ 3.0k
15
votes
0
replies
6.4k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 3 months ago by 39k • written 10.9 years ago by 98k
20
votes
5
replies
6.3k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 8 weeks ago by 39k • written 6.9 years ago by ★ 1.5k
8
votes
2
replies
6.3k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 16 months ago by 39k • written 8.6 years ago by 12k
8
votes
12
replies
6.2k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 8 weeks ago by 39k • written 7.0 years ago by 13k
14
votes
2
replies
6.2k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 9 weeks ago by 39k • written 7.8 years ago by ★ 2.9k
5
votes
5
replies
6.1k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 18 days ago by 39k • written 5.6 years ago by ▴ 130
19
votes
9
replies
6.1k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 3 months ago by 39k • written 10.0 years ago by 9.6k
6
votes
0
replies
6.0k
views
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
29
votes
5
replies
6.0k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 3 months ago by 39k • written 9.7 years ago by ★ 4.3k
4
votes
1
reply
5.9k
views
Tutorial: Chip-Seq Data Analysis Tutorial
chip-seq
updated 3 months ago by 39k • written 11.1 years ago by ▴ 360
16
votes
6
replies
5.8k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 1.7k
23
votes
19
replies
5.8k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
fastq mutation cancer target
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 2.4k
20
votes
7
replies
5.7k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 11 weeks ago by 39k • written 4.6 years ago by ▴ 750
14
votes
7
replies
5.6k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 11 weeks ago by 39k • written 7.1 years ago by ★ 3.3k
22
votes
2
replies
5.6k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 2.1k
34
votes
4
replies
5.6k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 6 months ago by 39k • written 7.9 years ago by ▴ 370
18
votes
2
replies
5.5k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 23 days ago by 39k • written 6.1 years ago by 5.2k
6
votes
3
replies
5.4k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 3 months ago by 39k • written 10.9 years ago by 98k
34
votes
15
replies
5.3k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
13
votes
6
replies
5.3k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 weeks ago by 39k • written 7.0 years ago by 14k
21
votes
10
replies
5.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 11 weeks ago by 39k • written 2.8 years ago by 12k
9
votes
2
replies
5.2k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 8 weeks ago by 39k • written 7.0 years ago by ▴ 140
7
votes
0
replies
5.1k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 3 months ago by 39k • written 11.0 years ago by ▴ 120
12
votes
31
replies
5.1k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 12 weeks ago by 39k • written 3.8 years ago by 7.9k
0
votes
2
replies
5.1k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 19 months ago by 39k • written 8.9 years ago by 9.6k
3
votes
2
replies
5.0k
views
Tutorial: Reorder Vcf Files
vcf
updated 3 months ago by 39k • written 10.1 years ago by ▴ 60
357 results • Page 3 of 8
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Answer: How to calculate TPM from featureCounts output
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Answer: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
A: How To Predict Pseudogenes In A Genome
How To Predict Pseudogenes In A Genome
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Recent Replies
Answer: Getting species names and taxa id from assembly accession number by MirianT_NCBI ▴ 580
Hi, As an alternative, you could use [NCBI Datasets][1] for this task. NCBI Datasets allows users to retrieve metadata reports in JSON or…
Comment: Optimum setting for local blastp for ~10K sequences by sodiumnitrate ▴ 20
Thank you for the info! It turned out that running all 10k at once is actually faster than running one or two at a time!
Answer: Installation of PPFinder by GenoMax 129k
Since the software is still [**listed on the Brent lab**][1] website your best bet would be to email the investigator and ask that they fix…
Comment: How to calculate TPM from featureCounts output by rpolicastro 12k
If you want to go that route, yes.
Comment: Difference between USCS exon coordinates and ensembl by ATpoint 72k
What did you download from UCSC? 1-off usually means one file is zero-based and the other 1-based. BED files from UCSC are 0-based, Ensembl…
Comment: Alignment of case vs. control from different origin by sativus • 0
Thank you kindly for the explanation, it is highly appreciated. I suppose i was a bit confused as you quite often see people validating the…
Answer: Gene enrichment analysis by nux ▴ 10
Hello. For this you have to select 'hyper' as your method and then provide a complete list of genes which both include the candidate and no…
Comment: CNNScoreVariants Error by bestone ▴ 10
Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.
Comment: Impute haplotypes (ImputePipelinePlugin) execution error - PHG by jrodrigu • 0
Thank you so much. I made the suggested changes. However, I still have the same problem. Please check the new log file. https://github.c…
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
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