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Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 9 hours ago by 40k • written 9.9 years ago by ★ 7.7k
18
votes
22
replies
8.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 5 days ago by ▴ 20 • written 3.8 years ago by 8.2k
36
votes
5
replies
5.8k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 19 days ago by ▴ 20 • written 8.2 years ago by ▴ 410
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 22 days ago by 134k • written 3.4 years ago by 77k
0
votes
1
reply
183
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 15 days ago by 77k • written 15 days ago by ▴ 30
1
vote
0
replies
173
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 14 days ago by 40k • written 14 days ago by 157k
6 results • Page 1 of 1
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Comment: demultiplexing with guppy_basecaller and guppy_barcoder using --detect_mid_stran
A: What'S The Difference Between Cds And Orf?
What'S The Difference Between Cds And Orf?
Answer: Filtering transcription factor and HOMER and ENCODE
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore
Answer: Number of accessible regions included by DESeq2 to generate the PCA plot with th
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Recent Replies
Comment: Splitting VCF/BCF file into seperate gene files by barslmn ★ 1.8k
What exactly proving difficult? Whats the results you're getting and what you like to get? Also you can use code sample to format your cod…
Comment: Troubles launch IGV on Linux(Debian) by barslmn ★ 1.8k
> I am on wayland. Is this a problem? Could be. Can you try it with Xorg? [You can usually change to Xorg in your login manager.][1] …
Answer: Have some issues in running prokka on WSL by Philipp Bayer 7.9k
It looks like the conda-installed BLAST has issues with the system's ZSTD, which is probably some WSL weirdness. You *might* be able to fix…
Comment: Network analysis with cytoscape by Chris ▴ 180
Sure, the network represents the different expressed genes in my RNA-seq. I choosed string protein query.
Comment: Network analysis with cytoscape by Yogi ▴ 40
A few questions. 1. What does the network represent? 2. Can you insert a high level picture of the network (or pictures) if you want to zo…
Answer: Chip-Seq and correlation of bam file by jared.andrews07 ★ 15k
Use [deepTools' plotCorrelation function](https://deeptools.readthedocs.io/en/develop/content/tools/plotCorrelation.html).
Answer: Transcription factor co-localization p-values by jared.andrews07 ★ 15k
[regioneR](https://bioconductor.org/packages/release/bioc/html/regioneR.html) seems to be what you want.
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data by LChart 3.4k
> Our major biological questions are: to have a general comparison of cancer vs normal “treatment” conditions; In addition if doable, to co…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thanks @luffy! Great material but seem they didn't mention how to customize the background genes depend on our data.
Comment: CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM by camillab. ▴ 140
I have calculate from this [tutorial][1]. so basically it retrieve the normalized counts matrix using `Deseq2` . Do you think it is correct…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by GenoMax 134k
`dorado` can't demultiplex data as yet (v.0.3.4). Also no adapter trimming. So something to keep in mind if you are switching. To address …
Comment: Frustrated with DEA results by dsull ★ 4.7k
Let the data speak. If there's no difference, then there's no difference. Human clinical data is always messy and unpredictable, especiall…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Ram 40k
I don't think they bought the Mac Studio just for the MiniON. If they did, that might be overkill. All things considered, I'd prefer an App…
Comment: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by ATpoint 77k
Wondering why investing all that money for such an overpriced piece of hardware. You could get an equivalent Windows or Linux workstation f…
Answer: Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore by Christopher ▴ 10
I'm using a Mac Studio with M1 Ultra chip to sequence with a MinION Mk1B now and it's working great! Fast basecalling and adaptive sequenci…
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