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412 results • Page 5 of 9
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Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by 82k • written 4 months ago by ▴ 120
0
votes
2
replies
2.6k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 2.1 years ago by 44k • written 9.3 years ago by ▴ 70
18
votes
2
replies
10k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.2 years ago by 44k • written 9.6 years ago by ▴ 860
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 2.3 years ago by 44k • written 9.5 years ago by 12k
3
votes
2
replies
2.9k
views
Tutorial: Running fastq_screen on your data
fastqscreen
2.2 years ago by rohitsatyam102 ▴ 870
4
votes
2
replies
3.0k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
4
votes
2
replies
3.6k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 14 months ago by 44k • written 8.3 years ago by ★ 2.5k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 19 months ago by ▴ 830 • written 2.7 years ago by ▴ 360
1
vote
2
replies
908
views
Tutorial: How to ask computational biology questions
computational-biology
updated 11 months ago by 44k • written 11 months ago by ★ 3.9k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 15 months ago by 44k • written 12.1 years ago by ▴ 540
1
vote
2
replies
3.3k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 19 months ago by 44k • written 8.8 years ago by ▴ 10
3
votes
2
replies
5.3k
views
Tutorial: Reorder Vcf Files
vcf
updated 15 months ago by 44k • written 11.0 years ago by ▴ 60
7
votes
2
replies
3.6k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 15 months ago by 44k • written 11.6 years ago by 11k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by 44k • written 7.1 years ago by ▴ 650
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 15 months ago by 44k • written 11.7 years ago by 100k
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 12 months ago by 44k • written 7.1 years ago by ▴ 30
7
votes
2
replies
2.0k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 44k • written 6.8 years ago by ▴ 90
8
votes
2
replies
1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 44k • written 9 months ago by ★ 2.5k
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 12 months ago by 44k • written 7.0 years ago by ★ 1.6k
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
10 months ago by Ming Tommy Tang ★ 3.9k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 13 months ago by 44k • written 8.0 years ago by ★ 1.1k
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 14 months ago by 44k • written 5.3 years ago by ▴ 10
7
votes
2
replies
1.8k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 44k • written 7.7 years ago by ★ 3.9k
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 44k • written 8.5 years ago by 20k
5
votes
2
replies
2.3k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 14 months ago by 44k • written 5.5 years ago by ▴ 50
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 15 months ago by 44k • written 12.0 years ago by 100k
6
votes
1
reply
2.6k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 14 months ago by 44k • written 9.6 years ago by 9.7k
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 15 months ago by 44k • written 12.0 years ago by ▴ 360
1
vote
1
reply
1.4k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 14 months ago by 44k • written 3.8 years ago by • 0
0
votes
1
reply
589
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
3
votes
1
reply
1.7k
views
Tutorial: Various youtube tutorials, including using proteomicsdb, finding adaptors, etc.
RNA Python
updated 13 months ago by 44k • written 8.2 years ago by ★ 1.1k
0
votes
1
reply
318
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 44k • written 4 months ago by ▴ 120
11
votes
1
reply
2.7k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 14 months ago by 44k • written 3.4 years ago by ★ 27k
2
votes
1
reply
487
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
568
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 12 months ago by 44k • written 6.8 years ago by ▴ 40
6
votes
1
reply
492
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
1.8k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 14 months ago by 44k • written 6.4 years ago by ▴ 10
22
votes
1
reply
3.2k
views
Tutorial: Introduction To R Course Materials Available
R
updated 16 months ago by 44k • written 12.1 years ago by 27k
2
votes
1
reply
2.8k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 16 months ago by 161k • written 16 months ago by ★ 2.2k
1
vote
1
reply
1.8k
views
Tutorial: Live webinar: Implications of Next Generation Sequencing in Molecular Diagnosis of Cancer on 28 Sep 2016
alignment sequencing genome SNP
updated 13 months ago by 44k • written 7.7 years ago by ▴ 70
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 12 months ago by 44k • written 6.9 years ago by ★ 1.6k
2
votes
1
reply
3.0k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 20 months ago by 44k • written 8.7 years ago by ★ 1.1k
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 14 months ago by 44k • written 4.1 years ago by ★ 2.5k
1
vote
1
reply
386
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
1.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 14 months ago by 44k • written 6.3 years ago by ▴ 10
2
votes
1
reply
62k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 22 months ago by 4.2k • written 22 months ago by ▴ 20
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by 44k • written 6.7 years ago by ▴ 110
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 12 months ago by 44k • written 6.4 years ago by ▴ 10
15
votes
1
reply
3.2k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 13 months ago by 44k • written 8.0 years ago by 20k
412 results • Page 5 of 9
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Answer: Question about samtools view flags (paired reads vs. properly paired reads)
Answer: Functional enrichment analysis for unique gene IDs
Comment: Super ehancers
Comment: Why does assigning genes with biomart give me different values than using a tran
Comment: Multiplexing for pooled CRISPR screen sequencing
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
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Recent Replies
Comment: Where are the illumina adapters on Trimmomatic take from? by bioinfo ▴ 150
Thank you for the explanation. Is it more appropriate then to use the sequence from the illumina documentation or the one from the github?
Comment: Question about samtools view flags (paired reads vs. properly paired reads) by mrk • 0
Thanks. What determines what constitutes a good distance? I have some targeted panel data and looking at flagstat, almost all reads are pai…
Comment: Where are the illumina adapters on Trimmomatic take from? by GenoMax 142k
Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
Comment: Allele count of 2 for homoplasmic MT variants in VCF by Ram 44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing by GenoMax 142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers by jared.andrews07 ★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by finch • 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples? by finch • 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Ram 44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Shukai • 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Ram 44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs by geneontologyhelp ▴ 410
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads) by Pierre Lindenbaum 161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
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