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:
10 months, 2 weeks ago
Joined:
2 years, 7 months 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 10 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 18 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 2.1 years 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 2.1 years 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 2.1 years 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 2.1 years 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 2.1 years 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 2.1 years 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 2.1 years 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 2.1 years ago by Hussain Ather940

Latest awards to Hussain Ather

Popular Question 14 months ago, created a question with more than 1,000 views. For What made you interested in Bioinformatics?
Scholar 14 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 18 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 2.0 years 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 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For Google announces DeepVariant
Scholar 2.4 years 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 2.4 years 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
Centurion 2.4 years ago, created 100 posts.
Teacher 2.4 years 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 2.5 years 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 2.5 years 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 2.5 years ago, created a post with more than 5 votes. For Google announces DeepVariant
Scholar 2.5 years 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 2.5 years 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
Rising Star 2.5 years ago, created 50 posts within first three months of joining.
Teacher 2.5 years 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 2.5 years 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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