User: goodez

gravatar for goodez
goodez460
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United States
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1 week, 3 days ago
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1 year, 1 month ago
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M.S. in Bioinformatics & Genomics. Always looking to expand my programming experience.

Posts by goodez

<prev • 138 results • page 1 of 14 • next >
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Comment: C: Loading bigiwg into an an array in javascript?
... Not sure about javascript unfortunately. But, in python there is a very helpful extension called pyBigWig. You can retrieve specific ranges as you desire and many other features. https://github.com/deeptools/pyBigWig ...
written 12 days ago by goodez460
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Comment: C: Identify RNA-seq reads containing polyA sequence
... Thanks, that is good to know. Please do share the reference if you find it again! ...
written 29 days ago by goodez460
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Comment: C: Identify RNA-seq reads containing polyA sequence
... Thanks! I have some additional questions then. Since it is stranded RNA-seq, the polyA will actually be stretches of `TTTTTT` right? Also I used `grep` to look for reads containing this, and many of the `TTTTTT` stretches are in the middle of a read. It doesn't seem possible that the polyA could be ...
written 29 days ago by goodez460
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Identify RNA-seq reads containing polyA sequence
... This may seem like a weird question, but we need to filter our RNAseq data for reads that contain polyA. The data is stranded RNA-seq, 50 bp reads. Would it be easier to find these reads before or after alignment? To be clear, the 50 bp read needs to contain a stretch of polyA, not just come from a ...
rna-seq written 29 days ago by goodez460 • updated 29 days ago by Buffo1.6k
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Comment: C: How to use edgeR to compare multiple conditions to reference condtiion
... Yes so 4 treatments, why is there only 3 coefficients (`2:4`)? ...
written 10 weeks ago by goodez460
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Comment: C: Rename files that are stored in a list in python
... I agree this isn't clear how it relates to bioinformatics, but here's some help (**If the paths are all the same length**) my_list=["path/A.txt", "path/B.txt", "path/C.txt"] [x[5:] for x in my_list] ['A.txt', 'B.txt', 'C.txt'] ...
written 12 weeks ago by goodez460
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Answer: A: ERCC Spike-in analysis without using any packages
... I recommend this package. I've used it for samples with spike-ins. Check out section 2.2 for an example where they're using ERCC spike-ins. https://bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf EDIT - I know your question was to avoid using a package, but it seems lik ...
written 3 months ago by goodez460
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Comment: C: for low coverage RNAseq how many reads assigned is the bare minimum for differen
... Depends on the genome. For example, you need more read depth for human alignments than you do for fly alignments. > What is the bare minimum number of reads I can use for differential > gene expression analysis? There's not really a bare minimum. Depends how sensitive your analysis is. Also ...
written 4 months ago by goodez460
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Comment: C: Explanation? Read depth, quality, and assembly accuracy in Methylome analysis co
... It's hard to say much without seeing the data, but it's probably fine. I recommend FastQC to check quality of the raw data. Sorry that I can't help much with methylation analysis. I'm not familiar with that. ...
written 4 months ago by goodez460
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Comment: C: Explanation? Read depth, quality, and assembly accuracy in Methylome analysis co
... Just one thing I'd point out is the difference between sequencing quality and mapping quality. Both have scores associated with them, but they mean different things. Sequencing quality is based on the confidence of correctly calling a given nucleotide. Mapping quality refers to the confidence of the ...
written 4 months ago by goodez460

Latest awards to goodez

Popular Question 24 days ago, created a question with more than 1,000 views. For Find consensus overlap between many bed files
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question
Scholar 6 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Appreciated 7 months ago, created a post with more than 5 votes. For C: SNPGenie: CDS does not have length that is divisible by 3
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question
Centurion 7 months ago, created 100 posts.
Scholar 8 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Meaning of Decimal points in ENST notation
Scholar 11 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Rising Star 11 months ago, created 50 posts within first three months of joining.
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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