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User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh • 310
Reputation:
310
Status:
Trusted
Location:
India
Website:
https://ag1805x.github...
Twitter:
ag1805x
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
5 years ago
Email:
a******@outlook.in

I am a Junior Research Fellow (JRF) at the Centre of Bioinformatics, University of Allahabad. I hold an undergraduate (B.Sc.) degree in Biotechnology from West Bengal University of Technology, India and a postgraduate (M.Sc.) degree in Bioinformatics from Alagappa University, India. My current research interests include stem cell bioinformatics, RNA-seq data analysis and network biology.

Posts by Arindam Ghosh

<prev • 201 results • page 1 of 21 • next >
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Comment: C: miRNAs interaction networks analysis
... For each of the tools mention above, except miRNet, I found they do not allow multiple queries at a time. miRNet seems to be good to retrieve interactions from a list of miRNAs/genes. Are there any other alternative tools that allow batch query? ...
written 10 weeks ago by Arindam Ghosh • 310
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Comment: C: htseq-counts output merge into one matrix ??
... Recheck on path and file format. ...
written 11 weeks ago by Arindam Ghosh • 310
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Comment: C: How to find p-value of the modules in WGCNA?
... The most observable thing that I saw for the MEs was that in turquoise module, the type1 samples had positive MEs (~ 0.14 or 0.06) while the type0 samples had negative MEs (~ -0.16 or -0.07 ). For other modules, no such uniformity were found. Also, for the turquoise module the correlation was high ...
written 12 weeks ago by Arindam Ghosh • 310
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Comment: C: How to find p-value of the modules in WGCNA?
... > the sample n is too small. n=45, it that still small? What would be the minimal number of samples that I should target? WGCNA tutorial mentions at least 20 samples. [In image, only top samples displayed by head()] For correlation test, I used the default Pearson's correlation: moduleTra ...
written 12 weeks ago by Arindam Ghosh • 310
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Comment: C: How to find p-value of the modules in WGCNA?
... Interestingly, in my case I observed the module that was the only significant module in correlation test (also the largest), failed in the glm fit test. Another module came out as significant which I was not expecting. Also the test with the largest module showed some warning as mentioned by @fernar ...
written 3 months ago by Arindam Ghosh • 310
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Comment: C: featureCounts for paired bam files and dealing with multimapping reads?
... A read from a gene can map to both the parent gene and as well as to a similar pseudogene. Removing ambiguous reads will under represent the parent gene even though it was expressed and counting them will over-represent the pseudogene. What do we do in such a situation? ...
written 3 months ago by Arindam Ghosh • 310
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Comment: C: Full GTF file vs Subset GTF file
... Bowtie2 with vsl (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931105/) ...
written 3 months ago by Arindam Ghosh • 310
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Comment: C: Full GTF file vs Subset GTF file
... Actually I tried with miRNA-seq data, aligned them to the reference genome and then in featureCounts used the full GTF (containing protein coding, lncRNA etc) and miRNA GTF. The miRNA GTF was created using: grep -E '#|gene_biotype "miRNA"' Homo_sapiens.GRCh38.84.gtf > Homo_sapiens.GRCh38.84 ...
written 3 months ago by Arindam Ghosh • 310
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Comment: C: Full GTF file vs Subset GTF file
... Anyway is this a logical way? Should this miRNA.gtf be used for read quantification? ...
written 3 months ago by Arindam Ghosh • 310
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Comment: C: Full GTF file vs Subset GTF file
... Create subset of Ensembl GTF file based on gene biotype grep -E '#|gene_biotype "miRNA"' Homo_sapiens.GRCh38.84.gtf > Homo_sapiens.GRCh38.84.miRNA.gtf ...
written 3 months ago by Arindam Ghosh • 310

Latest awards to Arindam Ghosh

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Appreciated 5 months ago, created a post with more than 5 votes. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
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