User: BehMah

gravatar for BehMah
BehMah30
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30
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New User
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Last seen:
3 months, 3 weeks ago
Joined:
2 years, 2 months ago
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e**********@gmail.com

Posts by BehMah

<prev • 39 results • page 1 of 4 • next >
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Comment: C: Can logCPM in edgeR be used to compare expression of different genes within samp
... Thanks, but l meant using CPM to compare genes within sample. ...
written 3 months ago by BehMah30
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Can logCPM in edgeR be used to compare expression of different genes within sample ?
... I did DE using edgeR and next want to compare expression between different genes (eg, A with B) using logCPM (edgeR output), so was wondering if 1- logCPM is expression average of all samples/conditions ? 2- ls logCPM a good representative of gene expression, like TPM, to compare expression of dif ...
R rna-seq written 3 months ago by BehMah30 • updated 3 months ago by grant.hovhannisyan1.5k
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Comment: C: How To Fetch Exon Sequence From Genomic Coordinates
... Ignore my last comment. I sorted it out thank you ATpoint :) ...
written 10 months ago by BehMah30
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Comment: C: How To Fetch Exon Sequence From Genomic Coordinates
... Thanks caggtaagtat! There is no assemble/annotation for rat (rnor 4) in biomart. There is just rnor 6 available :( ...
written 10 months ago by BehMah30
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Comment: C: How To Fetch Exon Sequence From Genomic Coordinates
... Thank you ATpoint. Sorry for Bedtools which was type error ;) I will give it a go. Just wondering if there there a way to get a single exon sequence (joint multiple exons) so I get only one sequence per each interval ? something like below: because each interval contain multiple exons. THANKS FOR Y ...
written 10 months ago by BehMah30
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How To Fetch Exon Sequence From Genomic Coordinates
... Hi Everyone :) I have a list of genomic coordinates and want to get only exon sequence for them. I can get the whole sequence (exon+intron) by Bedrolls getfasta but I want JUST exon sequences. Thank you :) ...
gene rna-seq written 10 months ago by BehMah30 • updated 10 months ago by ATpoint15k
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Comment: C: How to do Differential Expression for developmental series for normalised values
... Really appreciate your time and advices. ...
written 14 months ago by BehMah30
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Comment: A: How to do Differential Expression for developmental series for normalised values
... Thanks again Kevin. I am using R for all the stats. I think to return pvalue foe each gene I should change aov(gene.ex ~ group, data = my_data) a bit. ...
written 14 months ago by BehMah30
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Comment: C: How to do Differential Expression for developmental series for normalised values
... My pipeline is a bit different from normal way because Im doing DE for some non-coding RNA that are different from normal DE pipelines so I need to do statistics in my own way as a result can't use cufflinks/diff or DEseq/edgeR. Does ANOVA give Pvalue per gene(row)? or does it just give overall pva ...
written 14 months ago by BehMah30
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Comment: C: How to do Differential Expression for developmental series for normalised values
... Thanks Kevin for your time and answer. Following tophat, I normalised reads by depth of library to obtain RPM for each sample. In ANOVA, does it give pvalue per gene ? Also if compare pairwise using Wilcoxon works then why doing ANOVA then ? ...
written 14 months ago by BehMah30

Latest awards to BehMah

Popular Question 8 months ago, created a question with more than 1,000 views. For How to calculate RPM (reads per million mapped reads)?
Supporter 14 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For How to calculate RPM (reads per million mapped reads)?

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