User: Farbod

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Farbod3.1k
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2 years, 1 month ago
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s**********@yahoo.com

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

<prev • 562 results • page 1 of 57 • next >
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Comment: C: running BUSCO on all isoforms or longest isoform per gene?
... 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 Farbod3.1k
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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 Farbod3.1k
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running BUSCO on all isoforms or longest isoform per gene?
... 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 ...
assembly rna-seq written 11 hours ago by Farbod3.1k • updated 11 hours ago by lieven.sterck1.2k
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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 Farbod3.1k
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Answer: A: How to remove Bad Nucleotides represented by "N" from FASTA file by using UNIX?
... 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 Farbod3.1k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... 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 Farbod3.1k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Hi, I tried it, The blue spots change to red and red dot changed to blue! ...
written 4 months ago by Farbod3.1k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... 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 Farbod3.1k
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Comment: C: Showing FDR and log2FC in Volcano plot using R
... Thanks, In "aes(x=logFC, y =-log10(FDR)" I should use FDR or -log10(FDR) ? ...
written 4 months ago by Farbod3.1k
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Showing FDR and log2FC in Volcano plot using R
... 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) ...
R rna-seq volcano written 4 months ago by Farbod3.1k • updated 4 months ago by cpad01124.5k

Latest awards to Farbod

Popular Question 12 days ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 12 days ago, created a question with more than 1,000 views. For merging all coordinate-sorted bam files for Trinity genome-guided approach?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For how to map de novo assembly to reference genome ?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For showing row names and dendrogram in same side, using heatmap() or pheatmap()
Popular Question 4 months ago, created a question with more than 1,000 views. For DIAMOND blast imported into MEGAN6 has no taxonomic assignment
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
Student 11 months ago, asked a question with at least 3 up-votes. For DIAMOND blast imported into MEGAN6 has no taxonomic assignment
Scholar 13 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Appreciated 14 months ago, created a post with more than 5 votes. For A: Tools for categorize COG/KOG list
Teacher 16 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
Scholar 18 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Teacher 18 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
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Scholar 18 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Scholar 19 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Teacher 19 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
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Commentator 21 months ago, created a comment with at least 3 up-votes. For C: what is the evolutionary importance of existance of cancer gene(s) in other anim

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