User: Arindam Ghosh
Arindam Ghosh • 280
- Reputation:
- 280
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- Location:
- India
- Website:
- https://ag1805x.github...
- Twitter:
- ag1805x
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 day, 3 hours ago
- Joined:
- 4 years, 8 months 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.
Looking forward for new opportunities staring October 2020 and later.
Posts by Arindam Ghosh
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... 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 ...
written 2 days ago by
Arindam Ghosh • 280
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C: Batch correction in DESeq2
... > after adding the batch in the design formula, I also have to remove the batch effect, right?
Yes
here is a code that I tried for clustering on DESeq2 normalized counts:
dds <- DESeqDataSetFromMatrix(countData=counts, colData=factors, design = ~ Batch + Covariate)
dds <- DESeq(d ...
written 5 days ago by
Arindam Ghosh • 280
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C: miRNA differential expression
... That's a reasonably valid logic. I tried aligning with HiSat2 to the Ensembl reference genome and observed that overall alignment rate is ~60-70% with 40-50% unique alignment.
On a similar note, how do you deal with mRNA reads multi-mapping to different positions in the reference genome? Count all ...
written 7 days ago by
Arindam Ghosh • 280
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C: miRNA differential expression
... > "align against a database such as miRBase, not against the genome"
Any specific reason for this? We can align to reference genome (eg with Hisat2) and then extract only counts of miRNA (eg featureCounts) based on GTF annotation files (eg Ensembl). ...
written 8 days ago by
Arindam Ghosh • 280
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... Exactly! This is why I was curious to know why most studies separately use miRBase annotations for miRNA even though they are already in the Ensembl reference genome. So I believe there should not be any harm in using the Ensembl GTF file with featureCounts for estimating miRNA expression. ...
written 9 days ago by
Arindam Ghosh • 280
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... For RNA-seq (mRNA/lncRNA) data analysis, we can use reference genome and annotation from Ensembl (GRCh38). Can the same annotation file be used for miRNA-seq data analysis? Even though miRNA annotations are present in Ensembl, most works that I have come across use annotations from other databases l ...
written 11 days ago by
Arindam Ghosh • 280
• updated
11 days ago by
Astrid_Ensembl • 310
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C: microRNA- sequencing analysis
... Can we use annotations from Ensembl in step 3 as it contains co-ordinates from miRBase? ...
written 11 days ago by
Arindam Ghosh • 280
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... How about using the [contaminant list][1] supplied by FastQC as adapter list for trimmomatic? This helped me remove all contaminants that atleast FastQC can detect. I further combined this list with adopters supplied by Trimmomatic.
[1]: https://github.com/csf-ngs/fastqc/blob/master/Contaminants ...
written 14 days ago by
Arindam Ghosh • 280
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C: Tips for miRNA-Seq analysis
... Like if I have a 50bp read do I need to compulsorily trim to 35bp or just remove the adapters?
And for alignment, for mRNA data I use hisat2 with Ensembl gtf file. The gtf file contains details of miRNA as well. So is it necessary to separately download annotations from other sources? ...
written 14 days ago by
Arindam Ghosh • 280
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... I actually did that manually, but `factors()` would be better. `binarizeCategoricalVariable()` is another option with slightly different way of analysis as described by the WGCNA developers [here][1].
[1]: https://peterlangfelder.com/2018/11/25/working-with-categorical-variables/ ...
written 20 days ago by
Arindam Ghosh • 280
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