Moderator: Madelaine Gogol

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Madelaine Gogol5.1k
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Kansas City
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http://research.stower...
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@mmarchin
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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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News: bioinfo-core workshop at virtual ISMB 2020
... In case you aren't on the [bioinfo-core email list][1] or forgot, please take our [survey about ISMB this year][2], and let us know if you might have a lightning talk relevant to bioinformatics core facility members in your back pocket... More info below: ------------------------------------------- ...
news ismb conferences written 10 weeks ago by Madelaine Gogol5.1k
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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 13 months ago by Madelaine Gogol5.1k
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Comment: C: ISMB bioinfo-core workshop call for lightning talks
... Thanks! Much appreciated. ...
written 14 months 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 14 months ago by Madelaine Gogol5.1k • updated 14 months ago by genomax85k
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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 15 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 15 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 20 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 21 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 2.2 years 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 2.2 years ago by Madelaine Gogol5.1k

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Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Teacher 20 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 2.1 years ago, created a question with more than 10,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For ISMB 2015 biostars meetup attempt (Dublin)
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Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 2.8 years ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
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Popular Question 4.6 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
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