User: msimmer92

gravatar for msimmer92
msimmer92200
Reputation:
200
Status:
Trusted
Location:
Uruguay
Website:
https://www.linkedin.c...
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 4 months ago
Email:
m********@gmail.com

I am a biologist and neuroscientist from Uruguay, with both wet and dry lab experience, interested in neurogenetics/neuroepigenetics. For that, I dived into the world of bioinformatics during my undergrad and masters and I love it :). I am now starting my PhD in DZNE in Germany, planning to go into single-cell sequencing data analysis in neural systems. My main focuses are neuroscience, cool genomics/epigenomics fenomena, and trying to do science as accurate and good as possible. I really appreciate the existence of this platform where we can do this at a community level, way more interconnected than before!

Posts by msimmer92

<prev • 85 results • page 1 of 9 • next >
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Comment: C: Downsampling single-end human ChIP-seq data
... This would be my preference but unfortunately the guys that produce this data ran out of tissue and getting more is not easy. But thank you! Additionally, I want to say I tried the downsampling and the results look the same (in the sense that the results I'm observing seem to be so strong and the Di ...
written 6 weeks ago by msimmer92200
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Comment: C: Get all gene symbol in kegg pathway with clusterProfiler
... @Guangchuang Yu After doing the KEGG pathway analysis with ClusterProfiler and get the dotplot with the pathways, I would like to have a list with the genes so I can take a look (not all the genes in a given pathway, but the specific genes that had appeared in my pathway analysis). How can I do tha ...
written 6 weeks ago by msimmer92200
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Comment: C: Downsampling single-end human ChIP-seq data
... Thank you ! It's good to know (point 1)). Yeah, I will do what you suggest in 2). Answering your question, these numbers are after samtools markdup and filtering out those alignments with MAPQ below 30 (so keeping uniquely mapped reads only). These read numbers you see in the plot I took them from c ...
written 7 weeks ago by msimmer92200
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Comment: C: Downsampling single-end human ChIP-seq data
... Yes, sorry. These are samples from humans with different disease stages and then controls (groups A-H, one of them is control and the others incremental stages). H is control, then A is the first mild stage and E is the worst. The idea is to call peaks with MACS2 and do differential binding analysis ...
written 7 weeks ago by msimmer92200
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Downsampling single-end human ChIP-seq data
... The sequencing of this ChIP-seq H3K4me3 experiment (human, single-end 50bp) has a problem with the number of reads per sample. The person that did the sequencing did not arrange correctly the samples in the lanes, causing the bias you see in the picture (first, upper one). I am trying to "rescue" it ...
chip-seq downsampling subsampling written 7 weeks ago by msimmer92200 • updated 7 weeks ago by colin.kern320
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Comment: C: How to properly organize a DiffBind analysis to normalize data across conditions
... (sorry for the bunch of questions, I don't know if I should make another post about only this?) I also have a question about interpreting the pairwise MA plot that's produced by diffbind (dba.plotMA()). I'm new to this type of plots, so I showed it to a mathematician that I know. He said he would ex ...
written 11 weeks ago by msimmer92200
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Comment: C: How to properly organize a DiffBind analysis to normalize data across conditions
... Another question: yes, I use DEseq2. Do you recommend it or EdgeR? ...
written 11 weeks ago by msimmer92200
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Comment: C: How to properly organize a DiffBind analysis to normalize data across conditions
... Thank you for the script, I will check it out ! But what about if I am interested in comparing A vs B as well? (this is my main concern, that I can compare A and B being sure all A and B samples are properly normalized). For example, make MA and volcano plots for the pairwise comparisons of conditio ...
written 11 weeks ago by msimmer92200
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How to properly organize a DiffBind analysis to normalize data across conditions (ChIP-seq)
... Hello, I was wondering how the DiffBind normalization works when you have different conditions, and what's the proper way to organize the analysis according to that, since I noticed certain differences (I'll illustrate with an example). Imagine I have the following groups of replicates (ChIP-seq da ...
R diffbind chip-seq written 11 weeks ago by msimmer92200 • updated 11 weeks ago by ATpoint21k
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... Ok , thank you very much ! ...
written 11 weeks ago by msimmer92200

Latest awards to msimmer92

Voter 5 months ago, voted more than 100 times.
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 14 months ago, voted at least 25 times.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Error: --fst requires at least two nonempty clusters.

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