Limit : all time
all time today this week this month this year
411 results • Page 4 of 9
Sort: replies
Rank Views Votes Replies
2
votes
3
replies
572
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
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
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
74
votes
3
replies
39k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.4 years ago by 43k • written 9.8 years ago by 100k
3
votes
3
replies
2.8k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 14 months ago by 43k • written 2.0 years ago by ★ 4.3k
19
votes
3
replies
14k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 21 months ago by 43k • written 8.2 years ago by ★ 9.4k
0
votes
3
replies
53k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 12 months ago by 43k • written 7.9 years ago by ▴ 10
2
votes
3
replies
2.7k
views
Tutorial: It's about the journey, and not the destination
R network
updated 11 months ago by 43k • written 7.1 years ago by ★ 1.2k
1
vote
3
replies
3.2k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 12 months ago by 43k • written 7.7 years ago by ▴ 300
3
votes
3
replies
1.1k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 3 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
6
votes
3
replies
5.7k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 14 months ago by 43k • written 11.8 years ago by 100k
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
1
vote
3
replies
953
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
13 months ago by barslmn ★ 2.1k
45
votes
3
replies
13k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 12 months ago by 43k • written 8.1 years ago by ★ 3.2k
5
votes
3
replies
4.2k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 14 months ago by 43k • written 11.4 years ago by ▴ 80
6
votes
3
replies
4.5k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 13 months ago by 43k • written 5.5 years ago by ▴ 40
5
votes
3
replies
5.4k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 13 months ago by • 0 • written 6.5 years ago by ▴ 130
51
votes
3
replies
23k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 14 months ago by 43k • written 11.3 years ago by ▴ 300
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 11 months ago by 43k • written 6.3 years ago by ▴ 100
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 9 days ago by 6.4k • written 16 months ago by ▴ 130
13
votes
3
replies
5.1k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 23 months ago by 43k • written 9.1 years ago by ▴ 860
0
votes
3
replies
2.5k
views
Tutorial: Automatic Primer Design
Assembly sequence
updated 20 months ago by 43k • written 8.5 years ago by ▴ 40
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.6 years ago by 3.2k
9
votes
2
replies
5.5k
views
Tutorial: From Data import to Normalization in Microarray Analysis using in R (Part I)
gene R
updated 12 months ago by 43k • written 7.9 years ago by ▴ 140
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
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
45
votes
2
replies
37k
views
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
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
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
2
votes
2
replies
2.1k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 13 months ago by 43k • written 3.8 years ago by 3.2k
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 7.0 years ago by ★ 9.4k
22
votes
2
replies
5.8k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 19 months ago by ▴ 40 • written 3.0 years ago by 8.5k
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 12 months ago by 43k • written 7.6 years ago by ★ 3.9k
3
votes
2
replies
2.9k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.1 years ago by rohitsatyam102 ▴ 850
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 7.0 years ago by 27k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 12 months ago by 43k • written 7.9 years ago by ★ 1.1k
18
votes
2
replies
10.0k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.1 years ago by 43k • written 9.5 years ago by ▴ 860
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
4 months ago by GenoMax 141k
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
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
87
votes
2
replies
59k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by 43k • written 10.8 years ago by 11k
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.6k
15
votes
2
replies
3.0k
views
Tutorial: Introduction to bedtools.
bedtools
updated 13 months ago by 43k • written 9.4 years ago by 12k
3
votes
2
replies
534
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 3 months ago by ▴ 120
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 11 months ago by 43k • written 7.1 years ago by ▴ 30
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 13 months ago by 43k • written 4.9 years ago by ★ 9.4k
6
votes
2
replies
1.6k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.7 years ago by Kevin Blighe 87k
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 82k
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
411 results • Page 4 of 9
Recent Votes
Comment: NGS forensics: how to know if data is fabricated
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: How many reads for WGS Sequencing?
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Recent Locations • All
South Korea, just now
Australia, 3 minutes ago
USA, 3 minutes ago
Bologna, 6 minutes ago
United States, 6 minutes ago
Pakistan, 6 minutes ago
Palau, 7 minutes ago
Recent Awards • All
Teacher to Mensur Dlakic ★ 27k
Teacher to Jeremy Leipzig 22k
Popular Question to AshleeThomson ▴ 80
Popular Question to michael.flower.14 ▴ 180
Popular Question to Nitin Narwade ★ 1.6k
Popular Question to carlopecoraro2 ★ 2.5k
Popular Question to rj.rezwan • 0
Recent Replies
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 540
Working on it - it's actually a bit difficult. Low coverage of ribosomal proteins. Low coverage of housekeeping genes ...I'm trying to find…
Comment: NGS forensics: how to know if data is fabricated by noodle ▴ 540
I'm a bit against pubpeer - have you ever posted there? My gripe with them is that the posts are heavily moderated and EDITED to the point…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
Thanks Mensur! I'd add that in 9 out of 10 cases, you won't receive a reply to a request for raw data. That's just how scientists are, does…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
I had downloaded the two files in a similar manner actually.
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
ok, i'll try to use fastp. I have only used trimmomatic and cutadapt till now and they dont identify on its own. Except the graph in fastqc…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
got it! even if i'm doing the assembly for paired end with both the files do i have set the threshold to 1000bp ?
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.4k
i've been in our org trying to push such a detector, our use-case is much more limited: I want to make simulated eDNA libraries as real as …
Answer: Differential Expression using Isoseq-supplemented reference transcriptome by Gordon Smyth ★ 7.0k
> What is the best method to test for differential abundance at the isoform level? Salmon returns TPM values instead of the counts which Li…
Answer: Finding batch and outlayers by Tigran • 0
![enter image description here][1] [1]: /media/images/aa60b9ef-b08c-4093-9f0d-fb656a5c
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Can you post an IGV screenshot of what this looks like?
Comment: NGS forensics: how to know if data is fabricated by benformatics 3.9k
Yeah some of the Illumina machines pre-trim adapters (not sure if this is still the standard). I've also definitely also seen quality-trimm…
Comment: PDB related issue by noodle ▴ 540
You can typically find much more useful info in the cif file, for example what you've found is called '_atom_site.pdbx_PDB_ins_code ' and d…
Comment: PDB related issue by Mensur Dlakic ★ 27k
The best way to find out is to read the original paper. My guess is that the residue has been crystallized in alternative conformations, wh…
Answer: NGS forensics: how to know if data is fabricated by Mensur Dlakic ★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing? by Mensur Dlakic ★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Traffic: 3786 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6