User: Farbod
Farbod • 3.1k
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- Joined:
- 2 years, 1 month ago
- Email:
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Hi, I love Biology and Genetics and I have done my PhD thesis on "sturgeon fish RNA-seq" as my MSc was in aquaculture. I am interested in miRNA and epigenetics, too. And having about 4 years of experience in the field of bioinformatics.
Posts by Farbod
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... Hi and thanks,
As genome duplication sometimes can result in similar genes with different function, do you think it is harmless to remove all other isoforms (duplicated genes, alternative splicing?), here?
I mean the species has in fact a high percentage of duplication, is it OK to decrease it i ...
written 11 hours ago by
Farbod • 3.1k
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Comment:
C: NGS data Analysis pipeline
... Dear dpktiwari168, Hi.
Your question is more about the description of application and usage of NGS technology in different fields, and you know, it should be described in many books and different point of view instead of a Biostars post (my idea).
By the way, maybe you can benefit [This][1] and th ...
written 11 hours ago by
Farbod • 3.1k
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... Hi Biostars,
In order to assess the completeness of de novo transcriptome assembly, I have used [BUSCO_v3][1].
As my assembly belongs to a fish I have used *[actinopterygii][2]_odb9* as my **lineage** dataset.
I have ran BUSCO **once** on my whole assembly (in [Trinity][3] usually most genes have ...
written 11 hours ago by
Farbod • 3.1k
• updated
11 hours ago by
lieven.sterck • 1.2k
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Answer:
A: Bioinformatics Contest 2018
...
"We are happy to announce that **registration** for Bioinformatics Contest 2018 is **now open**. Qualification round starts on **February 3**, 2018. **Final** is on February 24.
Everything is online!"
http://bioinf.me/contest
***Bioinformatically Yours*** ...
written 3 months ago by
Farbod • 3.1k
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... Dear @*The Bright Star*, Hi and welcome to Biostars
Have you checked the [FASTA cleanup][1] by Pierre Lindenbaum in Biostars?
And also "[How to remove N from fasta sequences][2]"?
[1]: https://www.biostars.org/p/127714/
[2]: http://seqanswers.com/forums/showthread.php?t=26665 ...
written 4 months ago by
Farbod • 3.1k
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... Hi @cpad0112, I have another question and SORRY if it is not a bioinformatic one,
Is there any way to **change** these red and blue **colours of dots** (e.g into red and green)?
as I could not guess which part of my R script is resbomsible for that by looking at it's line of command.
Thanks ...
written 4 months ago by
Farbod • 3.1k
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... Hi, I tried it,
The blue spots change to red and red dot changed to blue! ...
written 4 months ago by
Farbod • 3.1k
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... Yes,
In original research I used FDR = 0.001 and log2FC =2 and I want to draw same volcano.
but
when I set the threshold as "`data$threshold = as.factor(data$-log10(FDR) < 0.001)` " it says :"Error in eval(expr, envir, enclos) : object 'threshold' not found"
when I use "`data$threshold = as ...
written 4 months ago by
Farbod • 3.1k
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... Thanks, In "aes(x=logFC, y =-log10(FDR)" I should use FDR or -log10(FDR) ? ...
written 4 months ago by
Farbod • 3.1k
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6 follow
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... Dear Biostars, Hi
In order to bioinformaticly show DEGs of RNA-seq in a volcano plot, I intend to use R, showing DEGs with **blue** spots and not significantly expressed genes with **red** dots.
The edgeR package which is embedded in Trinity software, uses **FDR (>0.001)** and log2FC (>2) ...
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For how to map de novo assembly to reference genome ?
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For merging all coordinate-sorted bam files for Trinity genome-guided approach?
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For showing row names and dendrogram in same side, using heatmap() or pheatmap()
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