User: msimmer92

gravatar for msimmer92
msimmer92230
Reputation:
230
Status:
Trusted
Location:
Uruguay
Website:
https://www.linkedin.c...
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 10 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 • 89 results • page 1 of 9 • next >
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Comment: C: If we use MACS2 do we need to remove duplicate sequences with samtools rmdup ?
... "macs2 is removing duplicate alignments" -> does this mean that it's analogous to do MAPQ filtering with samtools? Because I do this before calling peaks with MACS2 , but after reading this thread I am wondering if it's redundant. Thank you ! ...
written 6 weeks ago by msimmer92230
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... not from my side. still same problem ...
written 3 months ago by msimmer92230
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Comment: C: Heterogeneity from bulk ChIP-seq or ATAC-seq data
... Ok, thank you, both! I'll check out those papers. ...
written 3 months ago by msimmer92230
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Heterogeneity from bulk ChIP-seq or ATAC-seq data
... Nowadays, with single-cell ATAC-seq we can find subpopulations within a cell-type that has a different chromatin accessibility pattern. I was wondering if there is a way of having some glance of this kind of heterogeneity from bulk ChIP-seq or ATAC-seq. Maybe some way of clustering that, for example ...
heterogeneity chip-seq atac-seq clustering written 3 months ago by msimmer92230 • updated 3 months ago by jared.andrews075.0k
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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 7 months ago by msimmer92230
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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 7 months ago by msimmer92230
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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 8 months ago by msimmer92230
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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 8 months ago by msimmer92230
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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 8 months ago by msimmer92230 • updated 8 months ago by colin.kern820
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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 9 months ago by msimmer92230

Latest awards to msimmer92

Voter 12 months ago, voted more than 100 times.
Autobiographer 12 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 21 months ago, voted at least 25 times.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Error: --fst requires at least two nonempty clusters.

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