User: Sreeraj Thamban
Sreeraj Thamban • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- Indian Institute of Science Education and Research
- Last seen:
- 1 day, 17 hours ago
- Joined:
- 4 months, 3 weeks ago
- Email:
- s***************@iisertvm.ac.in
Posts by Sreeraj Thamban
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... Hello Bruce,
I did the DE analysis with and without multi-mapping reads and the results were almost similar.
Did you use mmquant? I read the paper and planning to give it a try in the future.
...
written 3 days ago by
Sreeraj Thamban • 30
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... Hi Biostars,
I used featureCounts to generate the counts table for the DEG analysis of my RNASeq data. I didn't count multi-mapping reads, but one of my libraries has 33% multi-mapped reads. I am afraid if I exclude the multi-mapping reads I will end up loosing a significant portion of the informati ...
written 4 days ago by
Sreeraj Thamban • 30
• updated
4 days ago by
bruce.moran • 280
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... Thank you Kevin this cleared my doubts. I have one more question, I took 1.3 as fold change cutoff to filter DEGs during the analysis, is 1.3 is an acceptable fold change? or should I increase?
Thank you ...
written 9 days ago by
Sreeraj Thamban • 30
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... Thank you Moulos, I will definitely give metaseqR a try. ...
written 9 days ago by
Sreeraj Thamban • 30
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... Hi all, During Differential gene expression analysis of RNASeq data (DESEq2 or Cufdiff) which is best method to filter differentially expressed genes? Should I go with all the genes having adjusted P value < 0.05 or should I filter them based on a log2 Fold change cut-off?
Thank you ...
written 10 days ago by
Sreeraj Thamban • 30
• updated
10 days ago by
Kevin Blighe • 1.2k
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... Hi lessismore, Thank you for your answer. Is there any standard guideline for valiadting the RNASeq data using qPCR? ...
written 25 days ago by
Sreeraj Thamban • 30
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... Hi, Biostars!
Can anyone tell me how to validate the RNA-Seq Differential gene expression data using qPCR?
How many genes should I select for qPCR validation?
Is there any criteria for selecting the differentially expressed genes for qPCR validation?
and finally what is the best method to visualize/ ...
written 25 days ago by
Sreeraj Thamban • 30
• updated
25 days ago by
lessismore • 170
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... For differential expression rna-seq analysis using gene ontology, following command was used to get topGOresults as
topGOresults <- runTest(topGOobject, algorithm = "weight01", statistic = "fisher")
topGOresults
and i got the output as follows
Description:
Ontology: MF
'wei ...
written 11 weeks ago by
Sreeraj Thamban • 30
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... https://www.biostars.org/p/250927/
You can follow this thread. ...
written 3 months ago by
Sreeraj Thamban • 30
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... Hi I used 150-200bp (best guess) as average fragment length in Kallisto but when I tried to reproduce the result from a tophat-cufflinks-cuffdiff pipeline the results shows very significant variation, but for paired-end reads, it was very consistent. So I think giving accurate fragment length is vi ...
written 4 months ago by
Sreeraj Thamban • 30
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