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Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 23 days ago by ▴ 20 • written 5.7 years ago by 87k
76
votes
72
replies
19k
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19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
7 days ago by Kevin Blighe 87k
87
votes
24
replies
23k
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17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 14 days ago by • 0 • written 3.5 years ago by 3.2k
5
votes
13
replies
1.4k
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Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 12 days ago by 82k • written 13 days ago by ★ 1.7k
4
votes
4
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433
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Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 5 days ago by ★ 1.7k • written 7 days ago by ★ 3.9k
7
votes
3
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2.9k
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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
1
vote
0
replies
191
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Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
14 days ago by Novogene ▴ 420
7 results • Page 1 of 1
Recent Votes
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: What analysis suitable to identify similarly expressed genes between two samples
Comment: Bacterial plasmid analysis
Comment: Problem with data downloaded from Short Reads Archive (SRA)
Comment: Problem with data downloaded from Short Reads Archive (SRA)
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Answer: What purposes can TPM values be used for? by jared.andrews07 ★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for? by Adam ▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped by i.sudbery 19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for? by dsull ★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for? by i.sudbery 19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis by Zamin Iqbal ▴ 10
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
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 …
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