User: Constantine

gravatar for Constantine
Constantine240
Reputation:
240
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Location:
USA
Last seen:
13 hours ago
Joined:
4 years, 7 months ago
Email:
c*******@mit.edu

Posts by Constantine

<prev • 40 results • page 1 of 4 • next >
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Comment: C: MNase-seq / fragment size selection
... This [paper][1] is a great example. [1]: https://www.cell.com/developmental-cell/fulltext/S1534-5807(14)00344-X ...
written 7 months ago by Constantine240
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Answer: A: MS Bioinformatics Project
... Sorry but if your Professor cannot help you find a project, I recommend you find another lab to pursue your Master's thesis. As a Master's student you expect to be given full guidance as it is an essential step before heading towards a PhD program. Asking for project ideas in a forum is not gonna he ...
written 15 months ago by Constantine240
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Answer: A: RNA-Seq time course DESeq2 analysis
... I recommend you do a differential expression analysis for each timepoint vs 0 in each condition. That is: 4h - 0 (WT) 8h - 0 (WT) 12h - 0 (WT) . . . 28h - 0 (mutant) and see if you find any statistical and biological significant changes (Normalise your raw counts for th ...
written 2.0 years ago by Constantine240
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Comment: C: extract small heatmap from big one deeptools
... if you run again the `plotHeatmap` function with the parameters `--kmeans 4` `--outFileSortedRegions mynewfile.bed` then your new bed file "mynewfile.bed" that is generated will be split into 4 different clusters. The genes you want are in the first cluster ...
written 2.4 years ago by Constantine240
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Comment: C: extract small heatmap from big one deeptools
... Sure ..should work this way ...
written 2.4 years ago by Constantine240
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Answer: A: extract small heatmap from big one deeptools
... Run it again with the parameter ` --outFileSortedRegions myfile.bed ` . The genes you want should be in the first cluster that comes up (I assume you have run it with a `--kmeans 4` ? ) ...
written 2.4 years ago by Constantine240
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Answer: A: Quantification of repeats expression
... Go to UCSC https://genome.ucsc.edu/ and under Tools > Table Browser Choose your genome and track (ideally RefSeq genes), and select "Output format: GTF" ...
written 2.5 years ago by Constantine240
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Comment: C: ChipSeq: merge bam file before peak calling
... Sorry for the late reply you need to parse replicates. For example python PePr.py -c Chip_R1.bam,ChIP_R2.bam -i Input_R1.bam,Input_R2.bam –n R1_sample1 –f bam --peaktype=sharp ...
written 2.8 years ago by Constantine240
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Answer: A: ChipSeq: merge bam file before peak calling
... You can use a peakcaller that accepts biological replicates I personally use [PePr][1] and I'm really happy with it. It has really high sensitivity and works very well both for sharp and broad regions [1]: https://github.com/shawnzhangyx/PePr ...
written 2.9 years ago by Constantine240
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Comment: C: MNase-seq / fragment size selection
... Yeap that's it. Sorry, hope it didn't sound confusing the way I addressed it ...
written 3.0 years ago by Constantine240

Latest awards to Constantine

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Quantification of repeats expression
Popular Question 9 weeks ago, created a question with more than 1,000 views. For MNase-Seq fragment size
Epic Question 3 months ago, created a question with more than 10,000 views. For Error in creating BAM index
Popular Question 7 months ago, created a question with more than 1,000 views. For MNase-Seq fragment size
Popular Question 11 months ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 12 months ago, created a question with more than 1,000 views. For NGS plot error
Appreciated 15 months ago, created a post with more than 5 votes. For A: MS Bioinformatics Project
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Quantification of repeats expression
Popular Question 18 months ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 19 months ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 19 months ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 22 months ago, created a question with more than 1,000 views. For NGS plot error
Great Question 23 months ago, created a question with more than 5,000 views. For Error in creating BAM index
Popular Question 2.1 years ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 2.2 years ago, created a question with more than 1,000 views. For NGS plot error
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Quantification of repeats expression
Popular Question 2.6 years ago, created a question with more than 1,000 views. For NGS plot error
Popular Question 3.0 years ago, created a question with more than 1,000 views. For IGV browser error
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Error in creating BAM index

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