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User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh • 350
Reputation:
350
Status:
Trusted
Location:
Finland
Website:
https://ag1805x.github...
Twitter:
ag1805x
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 4 days ago
Joined:
5 years, 4 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

<prev • 201 results • page 2 of 21 • next >
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Full GTF file vs Subset GTF file
... I have aligned raw RNA-seq reads to the Ensembl reference genome. I intend to quantify the expression using FeatureCounts of only say lincRNAs. What would be a better approach, use the full GTF file containing all types of RNAs or create a GTF containing only lincRNA and then use as input for Featur ...
ensembl featurecounts mirna-seq rna-seq written 7 months ago by Arindam Ghosh • 350 • updated 7 months ago by Shalu Jhanwar • 490
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Answer: A: DESeq2 for Differential gene expression
... Which tool did you use to generate expression values? I usually use FeatureCounts and I have not experienced float expression value yet. Also please check if the expression values are raw counts or has been pre-normalised. Float expression values are possible after normalisation. DESeq2 requires non ...
written 7 months ago by Arindam Ghosh • 350
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Comment: C: LncRNA Differential Expression and Analysis of lncRNA and mRNA co-expression.
... This seems something similar that I am planning to execute. Could you share some insights from your analysis that I should keep in mind while performing the analysis? ...
written 7 months ago by Arindam Ghosh • 350
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Answer: A: FastQC & trimming - RNA seq data
... A minimal quality trimming can be done to remove low quality bases (phred < 20) and adapters if present. For RNA-seq data I usually go by a rule to keep the minimum length to 80% of read length. I haven't come across any standard regarding the min len to set but longer reads are good for alignm ...
written 7 months ago by Arindam Ghosh • 350
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Comment: C: GO and KEGG from DESeq2 counts
... Just curious to know why edgeR works with GOana whille DESeq2 doesn't. Both gives a list of genes and I have performed GO analysis based on this list on web via DAVID and Panther. What's the difference with R packages? ...
written 7 months ago by Arindam Ghosh • 350
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Comment: C: Error in reading expression matrix
... Since the input file is `txt` while it is looking for `csv` file you have to specify the delimiter argument. Else re-save the file with extension `.csv`. that should work. ...
written 7 months ago by Arindam Ghosh • 350
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Comment: C: hisat2 mm10 low transcriptome mapping rate and low uniquely mapping rate
... Can you put up the FastQC GC content plot? ...
written 7 months ago by Arindam Ghosh • 350
0
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349
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Answer: A: hisat2 mm10 low transcriptome mapping rate and low uniquely mapping rate
... Have you checked the `--rna-strandness` option? ...
written 7 months ago by Arindam Ghosh • 350
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Comment: C: GTF/GFF for non-coding RNA
... Would be valid to use the gene_biotype specific gtf file for quantification after reads have been aligned to the reference genome? ...
written 7 months ago by Arindam Ghosh • 350
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HiSat2 vs BowTie2 for mapping miRNA-seq reads
... I am working with human miRNA-seq data. For alignment, I tried using two tools - BowTie2 and HiSat2 to align the clean reads to the reference genome GRCh38. Interestingly, I observed that HiSat2 provides more unique alignment that Bowtie2. The overall alignment rate was 10-20% higher in case of HiSa ...
mirna-seq bowtie hisat2 written 7 months ago by Arindam Ghosh • 350 • updated 3 months ago by Biostar ♦♦ 20

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Great Question 7 weeks ago, created a question with more than 5,000 views. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For in silico study of antimicrobial peptide
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Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Batch correction in DESeq2
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Popular Question 8 months ago, created a question with more than 1,000 views. For Protein structure prediction
Appreciated 9 months ago, created a post with more than 5 votes. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Student 10 months ago, asked a question with at least 3 up-votes. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 12 months ago, created a question with more than 1,000 views. For Protein structure prediction
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Scholar 16 months ago, created an answer that has been accepted. For A: What is the difference between gene FPKM and transcript FPKM values?
Popular Question 17 months ago, created a question with more than 1,000 views. For Bioinformatics for algae research
Popular Question 17 months ago, created a question with more than 1,000 views. For Can we directly correlate FPKM/TPM to expression?
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