User: Hussain Ather

gravatar for Hussain Ather
Hussain Ather940
Reputation:
940
Status:
Trusted
Location:
National Institutes of Health, Bethesda, MD
Website:
http://hussainather.com/
Twitter:
shussainather
Last seen:
3 months ago
Joined:
2 years ago
Email:
s************@gmail.com

Post-baccalaureate researcher interested in algorithm design and genomics. 

Comments represent my own, not necessarily my employer's.

Posts by Hussain Ather

<prev • 149 results • page 1 of 15 • next >
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Comment: C: Trimming adaptors with trimmomatic
... It may have to do with the CROP and MINLEN parameters. How long are your reads? ...
written 3 months ago by Hussain Ather940
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Answer: A: rna-seq expression analysis among several nonmodel species (Next step?)
... Maybe you could try making a density plot of FPKM values? There you could probably see a significant cutoff as a result of it. ...
written 10 months ago by Hussain Ather940
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Comment: A: Convert list of rs IDs from one format to another
... Can you give context on the IDs? How did you get them? What's the biological context? ...
written 17 months ago by Hussain Ather940
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Answer: A: Generating pileup from .bam file
... Hmmm have you looked at samtools mpileup? http://samtools.sourceforge.net/mpileup.shtml ...
written 17 months ago by Hussain Ather940
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Answer: A: Differential Expression from Quantile-Norm Data
... You should normalize them to a housekeeping gene. ...
written 17 months ago by Hussain Ather940
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Answer: A: Differential ChIP-Seq Analysis
... Look into deepTools bigWigCompare for comparing bigWig files based on the gene mapping ...
written 17 months ago by Hussain Ather940
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Comment: A: How can I convert from bed to bed12 format?
... You need more information than what's generally provided in the bed file. What programming language would you like to use? ...
written 17 months ago by Hussain Ather940
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Answer: A: How to do correlation analyses between RNAseq and ChIPseq library?
... 1) You could try normalizing the bins with respect to some larger value. 2) You could try taking the absolute value of ChIP-Seq profile to account for enrichment and depletion. ...
written 18 months ago by Hussain Ather940
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Comment: C: Assessing differentially expressed proteins between two samples
... 3 replicates for each test should be enough. ...
written 18 months ago by Hussain Ather940
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Answer: A: Using MACS2 for peak calling
... The default parameters generally perform pretty well. You could try running MACS multiple times with various parameters and visualizing the results in IGV or UCSC Genome Browser to determine how the parameters shape the peak-calling behavior. ...
written 18 months ago by Hussain Ather940

Latest awards to Hussain Ather

Popular Question 7 months ago, created a question with more than 1,000 views. For What made you interested in Bioinformatics?
Scholar 7 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Scholar 10 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Popular Question 18 months ago, created a question with more than 1,000 views. For Google announces DeepVariant
Scholar 21 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
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Teacher 22 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Scholar 22 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Appreciated 22 months ago, created a post with more than 5 votes. For Google announces DeepVariant
Scholar 22 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
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Teacher 23 months ago, created an answer with at least 3 up-votes. For A: When performing Fisher's exact test, should I consider all annotated or all dete
Scholar 23 months ago, created an answer that has been accepted. For A: When performing Fisher's exact test, should I consider all annotated or all dete
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