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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Answer: A: Convolution and deconvolution in gene expression

... This is a good paper to go through Wang, X., Park, J., Susztak, K., Zhang, N. R., & Li, M. (2019). Bulk tissue cell type deconvolution with multi-subject single-cell expression reference. Nature communications, 10(1), 1-9. Link: [https://www.nature.com/articles/s41467-018-08023-x][1] ![enter ...

written 17 days ago by Gjain ♦ 5.4k

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Comment: C: How to decide the parameters and parameter values when running ChIP-seq Peak Cal

... What issues are you facing? ...

written 17 days ago by Gjain ♦ 5.4k

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Comment: C: Why does BedTools Map operation produce all dots as output?

... This helped me even after 5 years ... tried various sorting but this one works perfectly .... thanks sort -k1,1 -k2n file > sortedFile Works great. ...

written 11 weeks ago by Gjain ♦ 5.4k

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Comment: C: HOMER HiC interactions

... Thanks for the paper and the link. I was not aware of that so that is good to know. I think you can try the standard HiC pipelines and a nice tutorial can be found here: [https://hms-dbmi.github.io/hic-data-analysis-bootcamp/#1][1] I hope this helps. [1]: https://hms-dbmi.github.io/hic-data-a ...

written 3 months ago by Gjain ♦ 5.4k

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Comment: C: HOMER HiC interactions

... Maybe you can try with bedtools to check if they are overlapping or not? ...

written 3 months ago by Gjain ♦ 5.4k

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149

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Comment: C: HOMER HiC interactions

... Are you sure you got different interactions and not duplicates? ...

written 3 months ago by Gjain ♦ 5.4k

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209

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Comment: C: Heterogeneity from bulk ChIP-seq or ATAC-seq data

... This paper might help: > Mars, J. C., Sabourin-Felix, M., Tremblay, M. G., & Moss, T. (2018). A > Deconvolution protocol for ChIP-Seq reveals analogous enhancer > structures on the mouse and human ribosomal RNA Genes. G3: Genes, > Genomes, Genetics, 8(1), 303-314. Link: [https://ww ...

written 3 months ago by Gjain ♦ 5.4k

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Comment: C: Calculating GC content from BAM file by BED file

... I am really amazed by the simplicity and awesomeness of this solution. Just one change I would like to make it to work would be | awk -v OFS="\t" '{n=length($6); gc=gsub("[gcGC]", "", $6); print $1,$2,$3,$4,gc/n}' As $5 is the count of the number of reads that overlapped with the bed region ...

written 6 months ago by Gjain ♦ 5.4k

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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 12 months ago by Gjain ♦ 5.4k

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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 12 months ago by Gjain ♦ 5.4k

Latest awards to Gjain

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Scholar 8 months ago, created an answer that has been accepted. For A: Sorting Chrs In [R]

Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Great Question 8 months ago, created a question with more than 5,000 views. For Chromosome Position From Ucsc Genome Browser

Appreciated 13 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Scholar 17 months ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?

Appreciated 19 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Scholar 2.2 years ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?

Popular Question 2.6 years ago, created a question with more than 1,000 views. For Bioinformatician/Biostatistician: Transcriptomics/Epigenetics in brain diseases (Goettingen, Germany)

Great Question 2.6 years ago, created a question with more than 5,000 views. For Chromosome Position From Ucsc Genome Browser

Scholar 2.8 years ago, created an answer that has been accepted. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics

Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bioinformatician/Biostatistician: Transcriptomics/Epigenetics in brain diseases (Goettingen, Germany)

Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes

Scholar 3.1 years ago, created an answer that has been accepted. For A: How to read Hi-C result from paper 'Bing Ren'

Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Popular Question 3.4 years ago, created a question with more than 1,000 views. For Chromosome Position From Ucsc Genome Browser

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

Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome

Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes

Student 5.0 years ago, asked a question with at least 3 up-votes. For Can Biostar Be Affected By Sopa?

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