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411 results • Page 4 of 9
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12
votes
11
replies
7.5k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.4k
12
votes
5
replies
2.5k
views
Tutorial: FASTA file split
fasta
updated 13 months ago by 43k • written 3.9 years ago by 8.6k
11
votes
3
replies
1.4k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 13 months ago by 43k • written 7.8 years ago by 7.1k
11
votes
0
replies
6.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 142k
11
votes
7
replies
2.3k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
13 months ago by barslmn ★ 2.1k
11
votes
1
reply
2.6k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 13 months ago by 43k • written 3.3 years ago by ★ 27k
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 11 months ago by 43k • written 3.2 years ago by ▴ 420
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 11 months ago by 43k • written 6.6 years ago by 87k
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
10
votes
4
replies
5.6k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
10
votes
0
replies
4.9k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 13 months ago by 43k • written 3.3 years ago by 142k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 13 months ago by 43k • written 4.8 years ago by 6.4k
10
votes
5
replies
24k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by 43k • written 5.8 years ago by ★ 9.4k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
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
10
votes
0
replies
2.6k
views
Tutorial: Introduction to Next Generation Sequencing (Part 1)
polony emulsion-pcr next-gen-sequencing
updated 18 months ago by 43k • written 8.8 years ago by ▴ 100
10
votes
2
replies
3.7k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 11 months ago by 43k • written 7.1 years ago by 27k
10
votes
1
reply
2.3k
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 13 months ago by 43k • written 4.1 years ago by ★ 2.5k
10
votes
3
replies
4.5k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 15 months ago by 43k • written 9.6 years ago by ▴ 860
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 5 weeks ago by 43k • written 6.2 years ago by 87k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by 43k • written 6.8 years ago by 100k
9
votes
9
replies
4.2k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 11 months ago by 43k • written 6.6 years ago by 87k
9
votes
0
replies
3.6k
views
Tutorial: Video: Intro to All New Features in IGB 8.2
R paired-end IGB
updated 2.2 years ago by 43k • written 9.4 years ago by ▴ 860
9
votes
2
replies
5.5k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
9
votes
0
replies
8.7k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 14 months ago by 43k • written 12.1 years ago by ▴ 540
9
votes
0
replies
4.4k
views
Tutorial: Analysis of dbGaP data on the cloud
AWS dbGaP Cloud
updated 21 months ago by 43k • written 8.2 years ago by 19k
9
votes
14
replies
3.7k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 18 months ago by ▴ 10 • written 2.2 years ago by ▴ 40
9
votes
3
replies
4.2k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 14 months ago by 43k • written 11.7 years ago by 100k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 13 months ago by 43k • written 9.5 years ago by ▴ 600
8
votes
7
replies
8.4k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 2.2 years ago by 43k • written 10.4 years ago by ★ 2.6k
8
votes
1
reply
1.4k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 13 months ago by 43k • written 3.1 years ago by 87k
8
votes
12
replies
6.8k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 13 months ago by 43k • written 7.9 years ago by 13k
8
votes
0
replies
2.7k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
3.1 years ago by rpolicastro 13k
8
votes
2
replies
6.6k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 2.2 years ago by 43k • written 9.5 years ago by 12k
8
votes
17
replies
3.2k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
alignment next-gen-sequencing RNA-seq
updated 20 months ago by 43k • written 8.6 years ago by ▴ 340
8
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 13 months ago by 43k • written 8.8 years ago by ▴ 430
8
votes
3
replies
2.8k
views
Tutorial: Free online interactive Ensembl training
ensembl training genome
updated 21 months ago by 43k • written 8.2 years ago by 23k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 14 months ago by 43k • written 10.0 years ago by ★ 1.8k
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
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 13 days ago by 6.4k • written 16 months ago by ▴ 130
7
votes
0
replies
5.3k
views
Tutorial: Mothur Analyzing 16S Of Ngs High Through-Put Sequencing
next-gen
updated 14 months ago by 43k • written 11.9 years ago by ▴ 120
7
votes
2
replies
3.5k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
7
votes
0
replies
3.0k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 13 months ago by 43k • written 8.0 years ago by ★ 5.1k
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
7
votes
3
replies
2.5k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 12 months ago by ▴ 110 • written 20 months ago by 87k
7
votes
8
replies
3.4k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 17 months ago by 43k • written 8.8 years ago by ★ 2.3k
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
0
replies
599
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
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
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
411 results • Page 4 of 9
Recent Votes
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
A: What is the difference between GRCh37 and hs37? And hg19?
A: Decoy In Reference Assembly
A: Decoy In Reference Assembly
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Recent Replies
Comment: Downsampling long-read BAM files by GenoMax 142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Estevão • 0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA) by atharvakarkare14 ▴ 20
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files by eesiribloom ▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by GenoMax 142k
Use `vdb-validate` included in `sratoolkit` to check your `*.sra` files for integrity.
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
This `fastq-dump --split-files *.sra` gives you fastq files. I am not sure how, with the given information, one might debug your problem. A…
Answer: What analysis suitable to identify similarly expressed genes between two samples by ATpoint 82k
DESeq2 has a "lessAbs" test which gioves you a pvalue that tests whether a fold change is **below** a user-defined threshold, see https://b…
Comment: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
In your table RawCounts, keep only the columns corresponding to condition 1 and the control. Edit the table sampleTable to align with your …
Comment: Problem with data downloaded from Short Reads Archive (SRA) by Begonia_pavonina ▴ 150
Thank you @atpoint, I did already investigate this error on the DADA2 github. It seems that the "BiocParallel" error can be due to multipl…
Comment: Discrepancy in read counts from fastq by GenoMax 142k
Try `reformat.sh` from BBMap suite and its sampling parameters. You may get a third answer. Programs do some approximations so it is probab…
Comment: Problem with data downloaded from Short Reads Archive (SRA) by ATpoint 82k
One cannot help you with this. The error is from R, yet you show not a single line of R code.
Comment: Bacterial plasmid analysis by Daria ▴ 10
I am the colleague! My tool groups together plasmids based on two genetic distances: containment (how much of the smaller plasmid's sequenc…
Comment: Subsetting and merging back Seurat Object brings different results by Bine ▴ 60
Ok I think I know what happened. The order of cells changed, otherwise its the same: ![image](https://github.com/satijalab/seurat/assets/7…
Answer: Bacterial plasmid analysis by shenwei356 8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding by ATpoint 82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
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