User: Sreeraj Thamban

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

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Dealing with multimapping reads in featureCounts
... 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 Thamban30
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Dealing with multimapping reads in featureCounts
... 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 ...
tophat featurecounts rna-seq written 4 days ago by Sreeraj Thamban30 • updated 4 days ago by bruce.moran280
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Comment: C: Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuf
... 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 Thamban30
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Comment: C: Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuf
... Thank you Moulos, I will definitely give metaseqR a try. ...
written 9 days ago by Sreeraj Thamban30
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Selecting Deferentially Expressed Genes in RNASeq data analysis - DESEq2 and Cuffdiff
... 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 ...
deseq2 rna-seq written 10 days ago by Sreeraj Thamban30 • updated 10 days ago by Kevin Blighe1.2k
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Comment: C: Validation of RNASeq Data - How to validate RNASeq DEGs using qPCR
... 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 Thamban30
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Validation of RNASeq Data - How to validate RNASeq DEGs using qPCR
... 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/ ...
deseq2 rna-seq written 25 days ago by Sreeraj Thamban30 • updated 25 days ago by lessismore170
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Retrieving Annotation data from runTest() created object
... 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 ...
deseq2 topgo gene ontology rna-seq written 11 weeks ago by Sreeraj Thamban30
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Answer: A: Gene set enrichment analysis cuffdiff output
... https://www.biostars.org/p/250927/ You can follow this thread. ...
written 3 months ago by Sreeraj Thamban30
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Comment: C: Getting average fragment length for single end reads
... 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 Thamban30

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