User: Irsan
Irsan • 6.8k
- Reputation:
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- Amsterdam
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- 2 days, 12 hours ago
- Joined:
- 6 years, 2 months ago
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PhD-student at Clinical Genetics, VU medical centre
Posts by Irsan
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... From now, 2 places left! Just signed up for the course. Looks promising! ...
written 22 months ago by
Irsan • 6.8k
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Comment:
C: Fastq Convert To Fasta
... OK, I have changed fasta to fastq ...
written 2.1 years ago by
Irsan • 6.8k
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2
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877
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Answer:
A: Heatmap trouble in R
... Because it scales the data. Use the scale="none" option ...
written 2.2 years ago by
Irsan • 6.8k
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6
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... Oh yeah that's right, forgot about that... ...
written 2.2 years ago by
Irsan • 6.8k
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... I would advice against it. Becuase of the three dimensions, some bars can block others. ...
written 2.2 years ago by
Irsan • 6.8k
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... In research, micro-arrays are on their return but in clinical diagnostics they are still used a lot, in particular array-CGH or SNP-arrays to determine germ line CNVs that predispose to disease. ...
written 2.2 years ago by
Irsan • 6.8k
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2.9k
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... A sample for which you now the ploidy = 2. So any non-cancer sample would be fine. I think most of the time in a SNP-array run such a sample is included, for example a male and female reference DNA sample. It depends all on your research context but most of the time, best scenario is when you have a ...
written 2.4 years ago by
Irsan • 6.8k
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2.9k
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... BAF = Y / (X + Y)
LRR = log2( (X + Y)sampleOfInterest / (X+Y)baselineSample)
But you might want to do some normalization first, possbily with beadstudio or with tQn normalization. See here http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-409 ...
written 2.4 years ago by
Irsan • 6.8k
0
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3
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5.4k
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... Hmm I still use star + htseq. I need to update my star version ...
written 2.5 years ago by
Irsan • 6.8k
1
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3
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... [HTseq][1] is another popular option
[1]: http://www-huber.embl.de/HTSeq/doc/overview.html ...
written 2.5 years ago by
Irsan • 6.8k
Latest awards to Irsan
Good Answer
10 months ago,
created an answer that was upvoted at least 5 times.
For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer
10 months ago,
created an answer that was upvoted at least 5 times.
For A: Random Genomic Regions Of A Given Length Distribution
Scholar
10 months ago,
created an answer that has been accepted.
For A: Bedtools Genomecoveragebed Usage : How To do per base coverage analysis for only
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Fastq Format Redundancy
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Cancer genomics journals
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Good Answer
15 months ago,
created an answer that was upvoted at least 5 times.
For A: If you have a chance to ask questions to the CEO of Illumina, what would you do?
Appreciated
15 months ago,
created a post with more than 5 votes.
For C: Conditional Coloring Of Heatmaps
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Revolution (?) in CNA detection using exome/targeted sequencing
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Fastq Format Redundancy
Great Question
16 months ago,
created a question with more than 5,000 views.
For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Does Bedops Have A Command Similar To The Bedtools Makewindows?
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Revolution (?) in CNA detection using exome/targeted sequencing
Good Answer
20 months ago,
created an answer that was upvoted at least 5 times.
For A: Coverage Calculation
Epic Question
22 months ago,
created a question with more than 10,000 views.
For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Monitor Hiseq Run Remotely Linux
Epic Question
2.2 years ago,
created a question with more than 10,000 views.
For Why Is Stranded Rna Seq Better Than Unstranded?
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Mysql-Query On Go-Database Ucsc Server
Commentator
2.4 years ago,
created a comment with at least 3 up-votes.
For C: What Is The Difference Between Structural Variants (Svs) And Copy-Number Variant
Good Answer
2.5 years ago,
created an answer that was upvoted at least 5 times.
For A: Coverage Calculation
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