User: goodez

gravatar for goodez
goodez460
Reputation:
460
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Trusted
Location:
United States
Last seen:
1 day, 12 hours ago
Joined:
1 year, 7 months ago
Email:
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M.S. in Bioinformatics & Genomics. Always looking to expand my programming experience.

Posts by goodez

<prev • 140 results • page 1 of 14 • next >
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Comment: C: merging two python dictionaries
... I use loops all the time in python. I just find comprehensions harder to read personally. In any case, I know mine works. As an aside, when I start worrying about being "pythonic", I don't even want to code anymore. Like why can't I just write something that works and is clear? ...
written 5 months ago by goodez460
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Answer: A: merging two python dictionaries
... Since they have the same keys, this would work: dict_3={} for i in dict_1: dict_3[i]=[dict_1[i], dict_2[i]] ...
written 5 months ago by goodez460
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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 6 months 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 6 months 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 6 months 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 6 months ago by goodez460 • updated 6 months ago by Buffo1.7k
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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 8 months 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 8 months 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 9 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 9 months ago by goodez460

Latest awards to goodez

Popular Question 5 months ago, created a question with more than 1,000 views. For Quick and easy way to get alignment stats from many SAM/BAM files?
Popular Question 6 months ago, created a question with more than 1,000 views. For Find consensus overlap between many bed files
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question
Scholar 12 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Appreciated 13 months ago, created a post with more than 5 votes. For C: SNPGenie: CDS does not have length that is divisible by 3
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question
Centurion 13 months ago, created 100 posts.
Scholar 14 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Meaning of Decimal points in ENST notation
Scholar 17 months ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
Rising Star 17 months ago, created 50 posts within first three months of joining.
Autobiographer 17 months ago, has more than 80 characters in the information field of the user's profile.
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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