Moderator: Gjain
Gjain ♦ 5.5k
- Reputation:
- 5,500
- Status:
- 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
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... 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
Gjain ♦ 5.5k
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... 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
Gjain ♦ 5.5k
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... What issues are you facing? ...
written 5 months ago by
Gjain ♦ 5.5k
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... 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
Gjain ♦ 5.5k
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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
Gjain ♦ 5.5k
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C: HOMER HiC interactions
... Maybe you can try with bedtools to check if they are overlapping or not? ...
written 7 months ago by
Gjain ♦ 5.5k
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Comment:
C: HOMER HiC interactions
... Are you sure you got different interactions and not duplicates? ...
written 8 months ago by
Gjain ♦ 5.5k
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... 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
Gjain ♦ 5.5k
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... 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
Gjain ♦ 5.5k
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1.8k
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... 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
Gjain ♦ 5.5k
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