User: msimmer92
msimmer92 • 230
- Reputation:
- 230
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- Trusted
- Location:
- Uruguay
- Website:
- https://www.linkedin.c...
- Last seen:
- 1 month, 2 weeks ago
- Joined:
- 2 years, 10 months ago
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- 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
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... "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
msimmer92 • 230
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... not from my side. still same problem ...
written 3 months ago by
msimmer92 • 230
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... Ok, thank you, both! I'll check out those papers. ...
written 3 months ago by
msimmer92 • 230
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... 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 ...
written 3 months ago by
msimmer92 • 230
• updated
3 months ago by
jared.andrews07 ♦ 5.0k
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... 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
msimmer92 • 230
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... @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
msimmer92 • 230
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... 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
msimmer92 • 230
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... 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
msimmer92 • 230
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... 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 ...
written 8 months ago by
msimmer92 • 230
• updated
8 months ago by
colin.kern • 820
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... (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
msimmer92 • 230
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For Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
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For Is there a way to do read filtering (MAPQ> certain value) on a BAM instead of SAM file?
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For Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
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For Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
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For The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
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For Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
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For A: Error: --fst requires at least two nonempty clusters.
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