Moderator: Gjain
Gjain ♦ 5.5k
- Reputation:
- 5,540
- Status:
- Trusted
- Location:
- Munich, Germany
- Website:
- http://www.linkedin.co...
- Twitter:
- @gauravjain49
- Last seen:
- 2 days, 15 hours ago
- Joined:
- 9 years, 4 months 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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... Hello Optimist!
We believe that this post does not fit the main topic of this site.
The post does not provide any details or fit the site in general.
For this reason we have closed your question. This allows us to keep the site focused
on the topics that the community can help with.
If you di ...
written 26 days ago by
Gjain ♦ 5.5k
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... An important point here is to make sure you do not loose reads with multi mapping as many piRNAs are similar sequences. ...
written 6 weeks ago by
Gjain ♦ 5.5k
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... You can either use featurecounts or multiBamSummary from deeptools to generate the gene expression table. ...
written 12 weeks ago by
Gjain ♦ 5.5k
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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 5 months 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 8 months ago by
Gjain ♦ 5.5k
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... What issues are you facing? ...
written 8 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 10 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 11 months ago by
Gjain ♦ 5.5k
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Comment:
C: HOMER HiC interactions
... Maybe you can try with bedtools to check if they are overlapping or not? ...
written 11 months ago by
Gjain ♦ 5.5k
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419
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Comment:
C: HOMER HiC interactions
... Are you sure you got different interactions and not duplicates? ...
written 11 months ago by
Gjain ♦ 5.5k
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