Moderator: Gjain

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Gjain5.5k
Reputation:
5,500
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Trusted
Location:
Munich, Germany
Website:
http://www.linkedin.co...
Twitter:
@gauravjain49
Last seen:
1 day, 23 hours ago
Joined:
9 years ago
Email:
g***********@gmail.com

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

<prev • 335 results • page 1 of 34 • next >
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Comment: C: peak summit in macs not the highest point
... Can you please show an example of such peak (Preferably an IGV screenshot) where the summit is not the highest point? ...
written 4 weeks ago by Gjain5.5k
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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 5 months ago by Gjain5.5k
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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 5 months ago by Gjain5.5k
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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 7 months ago by Gjain5.5k
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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 7 months ago by Gjain5.5k
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Comment: C: HOMER HiC interactions
... Maybe you can try with bedtools to check if they are overlapping or not? ...
written 7 months ago by Gjain5.5k
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Comment: C: HOMER HiC interactions
... Are you sure you got different interactions and not duplicates? ...
written 8 months ago by Gjain5.5k
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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 8 months ago by Gjain5.5k
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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 11 months ago by Gjain5.5k
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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 16 months ago by Gjain5.5k

Latest awards to Gjain

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome
Scholar 12 months ago, created an answer that has been accepted. For A: Sorting Chrs In [R]
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes
Great Question 12 months ago, created a question with more than 5,000 views. For Chromosome Position From Ucsc Genome Browser
Appreciated 17 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome
Scholar 21 months ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?
Appreciated 24 months ago, created a post with more than 5 votes. For A: Database Of Essential Genes
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes
Scholar 2.6 years ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?
Scholar 2.6 years ago, created an answer that has been accepted. For A: What Are The Exact Algorithms For Motif Discovery?
Great Question 3.0 years ago, created a question with more than 5,000 views. For Chromosome Position From Ucsc Genome Browser
Scholar 3.2 years ago, created an answer that has been accepted. For A: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to read Hi-C result from paper 'Bing Ren'
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Chromosome Position From Ucsc Genome Browser
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Database Of Essential Genes
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Greatest Achievements In Bioinformatics Other Than Human Genome
Good Answer 4.9 years ago, created an answer that was upvoted at least 5 times. For A: Database Of Essential Genes
Student 5.3 years ago, asked a question with at least 3 up-votes. For Can Biostar Be Affected By Sopa?

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