User: David

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David740
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Posts by David

<prev • 47 results • page 1 of 5 • next >
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Comment: C: Macs2 And Peak Calling On Chromosome X
... problem solved. MACS2 is working fine. A post-processing step on our side was making an error. ...
written 7.6 years ago by David740
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Comment: C: Macs2 And Peak Calling On Chromosome X
... yes. We use p-values as q-values just give either too many peaks or none when there are very few peaks. ...
written 7.6 years ago by David740
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Comment: C: Macs2 And Peak Calling On Chromosome X
... Thanks for this input. I will look into that. ...
written 7.6 years ago by David740
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Macs2 And Peak Calling On Chromosome X
... Hi, In my lab we are processing ChIP-seq all day and we switched to MACS2 beginning this year after using MACS1.4 for some time. We noticed yesterday that MACS2 never call peaks on chromosome X (and I suspect on chr Y too). We played with the p-value / q-value threshold all the way down to 1 (calli ...
macs chip-seq peak-calling written 7.6 years ago by David740
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Answer: A: Go Terms -- Is It Normal To Have Multiple Go Terms Associated With A Specific Ge
... If you want to visualise the percentage of shared gene between categories you can draw a heatmap like so ...
written 7.8 years ago by David740
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Comment: C: Interpreting Fastqc Results For Chip-Seq Data
... Thanks guys I will look into that. How does using: cat file1.fq file2.fq > file.fq can paste reads together? ...
written 7.8 years ago by David740
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Answer: A: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... There is a package for that called Heatplus http://www.bioconductor.org/packages/release/bioc/html/Heatplus.html ...
written 7.8 years ago by David740
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Comment: C: Interpreting Fastqc Results For Chip-Seq Data
... I found out that the quality trimming is performed by default. I am re-running it with a higher threshold. ...
written 7.8 years ago by David740
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Comment: C: Interpreting Fastqc Results For Chip-Seq Data
... Thanks for the hints. I will look into quality trimming. In our pipeline we keep duplicate reads but allow only unique matching at the alignment step. ...
written 7.8 years ago by David740
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Interpreting Fastqc Results For Chip-Seq Data
... Hello, I am processing a ChIP-seq experiment I downloaded from GEO (link). The SRA files are massive (39M sequences). It took me a while processing them. Briefly, I did SRA to fastQ format using fastq-dump then concatenated the 2 fastQ files with cat and ran fastQC a first time. I discover that the ...
chipseq fastqc chip-seq sequencing written 7.8 years ago by David740 • updated 7.8 years ago by Ido Tamir5.1k

Latest awards to David

Appreciated 6.6 years ago, created a post with more than 5 votes. For A: How To Convert List Of Entrez Ids Into Gene Name
Great Question 6.6 years ago, created a question with more than 5,000 views. For Interpreting Fastqc Results For Chip-Seq Data
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Macs2 And Peak Calling On Chromosome X
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Interpreting Fastqc Results For Chip-Seq Data
Teacher 6.6 years ago, created an answer with at least 3 up-votes. For A: How To Extract Highly Connected Subgraphs From A Gene Network Representation
Appreciated 7.3 years ago, created a post with more than 5 votes. For A: Gene Ontology Tool: David
Appreciated 7.3 years ago, created a post with more than 5 votes. For A: Bioinformatics Cores: How To Maintain Confidentiality Of Data
Good Answer 7.3 years ago, created an answer that was upvoted at least 5 times. For A: Gene Ontology Tool: David
Good Answer 7.3 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics Cores: How To Maintain Confidentiality Of Data
Good Answer 7.3 years ago, created an answer that was upvoted at least 5 times. For A: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: How To Remove Noise In Microarray Data?
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: How To Convert List Of Entrez Ids Into Gene Name
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: How To Find Out Whether There Is A Statistical Difference Between Two Sets Of St
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: How To Extract Highly Connected Subgraphs From A Gene Network Representation
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: Gene Ontology Tool: David
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics Cores: How To Maintain Confidentiality Of Data
Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?

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