User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh170
Reputation:
170
Status:
Trusted
Location:
India
Website:
https://ag1805x.github...
Twitter:
ag1805x
Last seen:
1 week, 2 days ago
Joined:
3 years, 11 months ago
Email:
a******@outlook.in

I am currently working as a Junior Research Fellow 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 • 135 results • page 1 of 14 • next >
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Comment: C: normalization RNA-seq data between different types of libraries
... Any update on this work? I am planning for something similar. ...
written 6 weeks ago by Arindam Ghosh170
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Answer: A: interval_list for hg38
... Just a few days back I was looking answer to the same question and hit upon [Kamil Slowikowski][1]'s method to generate for hg19. I modified this for GRCh38 and can be found [here][2]. [1]: https://gist.github.com/slowkow/b11c28796508f03cdf4b [2]: https://gist.github.com/ag1805x/55ba0d88f317f6 ...
written 6 weeks ago by Arindam Ghosh170
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Comment: C: Post alignment QC of RNA-seq data
... Yes. Using Picard I calculated the percentage of bases aligned to intronic and intergenic regions and found <15% for poly-A samples and for rRNA depleted samples it was ~25%. So I believe this should not be worrisome. And another query in addition to this, can the presence of ncRNA in rRNA samp ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: How to interpret Per sequence GC content module in FastQC for RNA-seq data?
... Yes. After trimming, few of the sequences that were reported as primer/adapter were removed and the once that remained have no known hit. I randomly selected few sequences and performed blast. For most there was no significant hit against human genomic + transcript db. While against all nucleotide I ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: Bimodal GC content
... Would the curve have multiple peaks if the sample is rRNA depleted? rRNA depleted samples would have several types of ncRNA besides mRNA that might alter the GC content. ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: Post alignment QC of RNA-seq data
... Is it usual for samples enriched by rRNA depletion to have higher intergenic/intronic content for human genome? I was working with publicly available data and observed this. Though it seems logical because these samples will contain ncRNA but I am not totally sure. ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: 3' Bias in RNASEQ data
... How do we deal with this during analysis? Should we ignore and proceed? ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: featureCounts for aligned reads
... should `allowMultiOverlap` be used or not? ...
written 7 weeks ago by Arindam Ghosh170
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Comment: C: FetureCounts low assigned rate and its weird total number counts?
... If " reads map to other parts of the genome (introns, intergenic)" should I remove the sample from downstream analysis? ...
written 8 weeks ago by Arindam Ghosh170
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Comment: C: Extremely low assigned reads in featureCounts
... if "many reads align outside of coding regions" should I proceed with what ever counts I get or should I discard the sample? ...
written 8 weeks ago by Arindam Ghosh170

Latest awards to Arindam Ghosh

Popular Question 21 days ago, created a question with more than 1,000 views. For Bioinformatics for algae research
Popular Question 21 days ago, created a question with more than 1,000 views. For Can we directly correlate FPKM/TPM to expression?
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Bioinformatics for algae research
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Epic Question 3 months ago, created a question with more than 10,000 views. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 5 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Popular Question 5 months ago, created a question with more than 1,000 views. For How to graphically tell if data has been normalized?
Popular Question 7 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Popular Question 7 months ago, created a question with more than 1,000 views. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Autobiographer 8 months ago, has more than 80 characters in the information field of the user's profile.
Epic Question 8 months ago, created a question with more than 10,000 views. For C program to find complementary of DNA sequence
Popular Question 9 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Student 9 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 11 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Great Question 11 months ago, created a question with more than 5,000 views. For Can anyone suggest a good tutorial to learn RNA-seq analysis?
Popular Question 11 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
Popular Question 13 months ago, created a question with more than 1,000 views. For Non-bonded atoms in PDB
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Popular Question 17 months ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence
Scholar 19 months ago, created an answer that has been accepted. For A: What is the difference between gene FPKM and transcript FPKM values?
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Popular Question 3.3 years ago, created a question with more than 1,000 views. For C program to find complementary of DNA sequence

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