Moderator: Madelaine Gogol

gravatar for Madelaine Gogol
Madelaine Gogol5.1k
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Location:
Kansas City
Website:
http://research.stower...
Twitter:
@mmarchin
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Google Scholar Page
Last seen:
1 month, 2 weeks ago
Joined:
9 years, 4 months ago
Email:
m********@gmail.com

I'm a Programmer Analyst in a bioinformatics core facility at Stowers Institute. I use R (and Perl, don't judge me) to munge and analyze data from all sorts of critters in all sorts of (usually sequencing) experiments.

Posts by Madelaine Gogol

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Comment: C: how can i download human ribosomal reference ?
... Yep, I have used ensembl biomart for this, as linked in the first comment. ...
written 8 weeks ago by Madelaine Gogol5.1k
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Comment: C: ISMB bioinfo-core workshop call for lightning talks
... Thanks! Much appreciated. ...
written 11 weeks ago by Madelaine Gogol5.1k
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Forum: ISMB bioinfo-core workshop call for lightning talks
... I'm an organizer of a workshop for [members of bioinformatics core facilities][1] at [ISMB/ECCB 2019][2] (Basel) and we are looking for a few more good lightning talks to round out our program. We'd love to get more talks on single-cell RNA-seq or nanopore if you have experience with that ([other p ...
forum conferences written 11 weeks ago by Madelaine Gogol5.1k • updated 11 weeks ago by genomax69k
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Comment: C: Is Biostar Killing The Bioinformatics Core?
... Well, this bioinformatics core employee is quite grateful that biostars exists. I have even found old answers that I made and forgot about. I also love teaching biologists to do their own analysis. If they ever don't need me anymore, I'll find something else interesting to do. : D ...
written 3 months ago by Madelaine Gogol5.1k
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Comment: C: disproportinate fastq sizes from bcl2fastq
... This one liner will show you some of the most common barcodes in your undetermined fastq file. Might help? zcat undetermined.fastq.gz | grep "^@" | sed "s/.*://g" | head -n 1000000 | sort | uniq -c | sort -n ...
written 3 months ago by Madelaine Gogol5.1k
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Comment: C: Run CCA in Seurat
... Add the arguments add.cell.id1="ctrl",add.cell.id1="stim" to your RunCCA call. This will append these onto your ids. ...
written 8 months ago by Madelaine Gogol5.1k
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Comment: C: navigate IGV to the points of interest
... Yeah, and then you could also use a batch file to automate jumping to those regions, maybe: https://software.broadinstitute.org/software/igv/batch ...
written 9 months ago by Madelaine Gogol5.1k
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Comment: C: lack of replicates in single-cell RNA-seq
... Huh, what would I do if I had a replicate! That would be cool! See if the clusters look "the same", I suppose, but if they don't, then what? Hmmmmmmm... ...
written 14 months ago by Madelaine Gogol5.1k
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Comment: C: which is good to study methylation among breast cancer patients; ChIP-Seq and Wh
... This feels more like a biology question... You may try seqanswers.com? I guess it depends on which aspects are more important to you, methylation or histone marks or what. You may be able to find some public data to get you started. ...
written 14 months ago by Madelaine Gogol5.1k
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Comment: C: Sequencing with 10X genomics
... You might want to look at http://10xqc.com/ ...
written 16 months ago by Madelaine Gogol5.1k

Latest awards to Madelaine Gogol

Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Epic Question 14 months ago, created a question with more than 10,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Popular Question 14 months ago, created a question with more than 1,000 views. For ISMB 2015 biostars meetup attempt (Dublin)
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 21 months ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Great Question 3.0 years ago, created a question with more than 5,000 views. For Nextseq for analysts
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Prophet 3.1 years ago, created a post with more than 20 followers. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Great Question 3.4 years ago, created a question with more than 5,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Commentator 3.9 years ago, created a comment with at least 3 up-votes. For C: Which Bachelor Should I Choose For A Position In Bioinformatics?
Good Answer 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For Short Read Mapping?
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm

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