User: Arindam Ghosh
Arindam Ghosh • 340
- Reputation:
- 340
- Status:
- Trusted
- Location:
- Finland
- Website:
- https://ag1805x.github...
- Twitter:
- ag1805x
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 weeks, 3 days ago
- Joined:
- 5 years, 3 months ago
- Email:
- a******@outlook.in
I am a Early Stage Researcher at the University of Eastern Finland, Kuopio. 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
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... 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 5 months ago by
Arindam Ghosh • 340
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... Recheck on path and file format. ...
written 5 months ago by
Arindam Ghosh • 340
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... 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 5 months ago by
Arindam Ghosh • 340
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... > 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 5 months ago by
Arindam Ghosh • 340
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... 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 6 months ago by
Arindam Ghosh • 340
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... 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 6 months ago by
Arindam Ghosh • 340
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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 6 months ago by
Arindam Ghosh • 340
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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 6 months ago by
Arindam Ghosh • 340
0
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1
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229
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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 6 months ago by
Arindam Ghosh • 340
0
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1
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229
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1
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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 6 months ago by
Arindam Ghosh • 340
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