User: Farbod

gravatar for Farbod
Farbod2.9k
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Location:
Montreal
Last seen:
3 days, 22 hours ago
Joined:
11 months, 2 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 • 487 results • page 1 of 49 • next >
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Comment: C: Fold Change accepts, FDR denies; which one to use ?
... Dear Devon Ryan, Hi and thank you. As an expert in this field, could you please mention a reference "paper" about this strategy (ignoring the FDR and using FC threshold) for me? ~ Best ...
written 8 days ago by Farbod2.9k
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Comment: C: Fold Change accepts, FDR denies; which one to use ?
... Dear WouterDeCoster, I am using the gonads of each gender. Trinity usually reports several isoforms for each gene. ...
written 8 days ago by Farbod2.9k
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Comment: C: Fold Change accept, FDR deny; which one to use ?
... 1- thank you for your complete explanation. I have 3 biological replication for males and 3 for females (So, 6 samples in total and I am comparing DEG between sexes). I have TMM values and Trinity have used it for matrix and heatmap creation. can I use the TMM values for my box-plot drawing ? t ...
written 8 days ago by Farbod2.9k
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Comment: C: Fold Change accept, FDR deny; which one to use ?
... Good question. ;-) In the gene level DEG analysis pipeline of Trinity, **FDR** for these 11 isoforms is **0.8** and the **log2FC** is **-0.6** toward the females (which **is not correct** because **(1)** most isoforms are up-regulated in males, **(2)** the other researches showed that this gene is ...
written 8 days ago by Farbod2.9k
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Comment: C: Fold Change accept, FDR deny; which one to use ?
... What do you mean by "heterogeneity " here ? would you kindly explain more for me, please? ...
written 8 days ago by Farbod2.9k
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Comment: C: Fold Change accept, FDR deny; which one to use ?
... Hi and thanks, This gene has about 11 isoforms, most of them (7) have FC from 0.5 to 5 in males but two of them have up-regulated FC from -0.6 to -1.2 in females. the FDRs are from 0.1 to 1. Do these extra information have any effect on your guidance? ...
written 8 days ago by Farbod2.9k
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Fold Change accepts, FDR denies; which one to use ?
... **Dear Biostars, Hi.** I have used DESeq2 for my RNA-seq DEG analysis (de novo assembly using Trinity, RSEM, DESeq2) I have used **FDR=0.05** as my threshold. Now I have some genes that in **similar researches** was up-regulated in one condition (e.g in males) but in my results the same gene has ...
fdr fc rna-seq deg written 8 days ago by Farbod2.9k • updated 8 days ago by Devon Ryan62k
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zero TMM : assembly error or biologically important phenomenon?
... Dear Biostars, Hi I have some transcripts (*RNA-seq/ illumina/ Trinity de novo assembly/RSEM*) **TMM** values that are zero for 3 **replications** of condition 1 (C1) and **two** of condition 2 (C2) . Does these transcriptes **worth** for further analysis and investigation or not? Example : C1a- ...
gene rna-seq written 20 days ago by Farbod2.9k
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News: Webinar on DNA-Seq Data Analysis : Feb 2017
... **[Webinar on DNA-Seq Data Analysis][1]** Abstract: DNA-Seq data can be analyzed and visualized using an extensive workflow in Strand NGS software. The software has been designed for the biologists. Strand NGS – supports analysis of whole exome, whole genome and targeted sequencing experiments. Th ...
next-gen dna-seq news written 21 days ago by Farbod2.9k
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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 5 weeks ago by Farbod2.9k

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