User: Farbod

gravatar for Farbod
Farbod2.9k
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Location:
Montreal
Last seen:
5 days, 18 hours ago
Joined:
10 months, 3 weeks ago
Email:
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 • 478 results • page 1 of 48 • next >
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Comment: C: How to discover condition-dependent SNPs in transcriptomic data where each genes
... Yes, it did. I really appreciate all your supports. In regard to my **#3** question, if "Most of SNPs are entirely meaningless/harmless" and "every individual differs on many position with other individuals (even in monozygotic twins)"; so **what is the usage of SNP collecting** in RNA-seq and **w ...
written 12 days ago by Farbod2.9k
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Comment: C: How to discover condition-dependent SNPs in transcriptomic data where each genes
... Dear @WouterDeCoster, thank you, Maybe I am not very well aware of what SNP means. I guess it means that it must be some substitution of one nucleotide in distinct populations or healthy/sick tissue/genes or responsible for two phenotypes ? 1- please correct me if it is not true. 2- I have 6 fas ...
written 12 days ago by Farbod2.9k
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Comment: C: How to discover condition-dependent SNPs in transcriptomic data where each genes
... Dear @Wouter, would you please have a look at the "[Detection genetic markers][1]" section for SNP detection from de novo transcriptome and help me about it ? [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133083/ ...
written 13 days ago by Farbod2.9k
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Comment: C: How to discover condition-dependent SNPs in transcriptomic data where each genes
... Dear @Wouter, Hi. Yes I simplified my other [similar question][1] about SNPs. I wonder how in some RNA-seq papers, the authors report their SNPs along DEGs, SSRs, TFs and etc. Are there any DE-SNPs discovery pipeline that I am not aware of ? This is the purpose of this question. ;-) [1]: ht ...
written 14 days ago by Farbod2.9k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... Hi, I have searched but I did not find any related topic. Thank you for your help. ...
written 14 days ago by Farbod2.9k
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Comment: C: Transcription Factor, Promoter dataset
... Dear Mojtaba, Hi Have you checked [AnimalTFDB][1] ? ~ Best [1]: http://bioinfo.life.hust.edu.cn/AnimalTFDB/ ...
written 15 days ago by Farbod2.9k
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How to discover condition-dependent SNPs in transcriptomic data where each genes has several isofofrms ?
... **Dear Biostars, Hi.** I have asked [similar question][1] but I have not received an acceptable answer or guideline, so I am asking it in other words : Imagine that I have done a de novo transcriptome assembly from RNA-seq data using Trinity (no reference genome). I have 3 biological replication ...
assembly next-gen rna-seq snp written 16 days ago by Farbod2.9k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... Dear Guangchuang, Hi I sometimes received the following error from the *nwk* files I have exported from **MEGA6**. Have you any idea about it ? > Error in read.tree(file = "2.nwk") : The tree has apparently > singleton node(s): cannot read tree file. Reading Newick file > aborted at ...
written 16 days ago by Farbod2.9k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... I have solve it as below, would you check it please : biocLite("ggtree", type = "source") #for solving the Error: StatTreeHorizontal was built with an incompatible version of ggproto. library(ape) library("ggplot2") library(ggtree) tree <- read.tree(file = "test.nwk") gg ...
written 17 days ago by Farbod2.9k
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Comment: C: ggtree: phylogenetic tree visualization and annotation
... Dear Guangchuang Yu, Hi Sorry for my simple question but would you please help me for importing a Newick file (e.g test.nwk) in *ggtree* for drawing phylogenic tree? I am using Rstudio. ~ Best ...
written 18 days ago by Farbod2.9k

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Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Can't open gz file
Scholar 12 weeks ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
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Scholar 3 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Scholar 4 months ago, created an answer that has been accepted. For A: mireap procedure short tutorial
Teacher 4 months ago, created an answer with at least 3 up-votes. For C: Can't open gz file
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