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User: Arindam Ghosh

gravatar for Arindam Ghosh
Arindam Ghosh • 170
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 Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170
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Comment: C: featureCounts for aligned reads
... should `allowMultiOverlap` be used or not? ...
written 7 weeks ago by Arindam Ghosh • 170
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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 Ghosh • 170
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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 Ghosh • 170

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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
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