User: Gjain

Bioinformatician with extensive experience in genomics and epigenomics. In-depth knowledge of computational biology and machine learning methodologies.

Specialties:
• Languages: Python, Perl, R, HTML/HTML5, PHP, Javascript, AJAX, Shell scripting, C/C++, Octave

• Big Data: Next generation sequencing, Statistical and bioinformatics data analysis, Machine learning algorithms

• High-throughput Assays: Chromosome Conformation Capture (3C)-based techniques (5C, Hi-C), ChIPseq, RNAseq

• Databases: MySQL, Oracle

• Other: UNIX/Linux, High performance cluster computing (HPCC), Linux server management, Vector graphics/illustration tools

Posts by Gjain

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Comment: C: normalization in single cell RNAseq

... I completely agree and also the limitations of having less than 80% zeros are there. Denoising tools can help to solve this problem. But yes, still a very new field. ...

written 5 months ago by Gjain ♦ 5.3k

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Answer: A: normalization in single cell RNAseq

... Hi, I would look into SCnorm package ([https://github.com/rhondabacher/SCnorm][1]). Paper link: [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473255/][2] Important point: > To evaluate the extent to which biases introduced during normalization affect the identification of DE genes, we appl ...

written 5 months ago by Gjain ♦ 5.3k

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Comment: C: mapping unmapped reads to viral genome using blast+

... Thanks for the information ...I will try Kraken2 ...

written 6 months ago by Gjain ♦ 5.3k

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Comment: C: mapping unmapped reads to viral genome using blast+

... Do you have a preference on one tool over another? ...

written 6 months ago by Gjain ♦ 5.3k

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Comment: C: What'S The Difference Between Cds And Orf?

... Is this the first citation for a biostars post? ...

written 10 months ago by Gjain ♦ 5.3k

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971

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Answer: A: When do you strictly need to know the adapter sequence to trim NGS data?

... This is a good question for the beginners who are starting with the NGS analysis. > In common short read sequencing, the DNA insert (original molecule to > be sequenced) is downstream from the read primer, meaning that the 5' > adapters will not appear in the sequenced read. But, if the fr ...

written 11 months ago by Gjain ♦ 5.3k

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Comment: C: Format Refseq Output Obtained From Ucsc Table Browser ?

... It will depend on the biological question you are interested in. You can choose the longest transcript or other criteria that fits your hypothesis. ...

written 12 months ago by Gjain ♦ 5.3k

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Comment: C: What server do you use?

... might very well be possible. The HPC staff can clarify this. ...

written 12 months ago by Gjain ♦ 5.3k

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690

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Comment: C: What server do you use?

... In that case, talking to the HPC staff about your scheduling problem might help ...

written 12 months ago by Gjain ♦ 5.3k

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Comment: C: What server do you use?

... Did you look into the interactive mode? This is what you have done in the past when you login into HPC and log to one node. ....You can use interactive mode to login to the node and run commands there. ...

written 12 months ago by Gjain ♦ 5.3k

Latest awards to Gjain

Appreciated 6 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Scholar 9 months ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?

Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Appreciated 12 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Scholar 19 months ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?

Popular Question 2.0 years ago, created a question with more than 1,000 views. For Bioinformatician/Biostatistician: Transcriptomics/Epigenetics in brain diseases (Goettingen, Germany)

Great Question 2.1 years ago, created a question with more than 5,000 views. For Chromosome Position From Ucsc Genome Browser

Scholar 2.2 years ago, created an answer that has been accepted. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics

Popular Question 2.4 years ago, created a question with more than 1,000 views. For Bioinformatician/Biostatistician: Transcriptomics/Epigenetics in brain diseases (Goettingen, Germany)

Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Appreciated 2.5 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Scholar 2.5 years ago, created an answer that has been accepted. For A: How to read Hi-C result from paper 'Bing Ren'

Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Popular Question 2.9 years ago, created a question with more than 1,000 views. For Chromosome Position From Ucsc Genome Browser

Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Student 4.4 years ago, asked a question with at least 3 up-votes. For Can Biostar Be Affected By Sopa?

Good Answer 4.4 years ago, created an answer that was upvoted at least 5 times. For A: Ethical Issues In Bioinformatics

Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics

Scholar 4.5 years ago, created an answer that has been accepted. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics

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