User: msimmer92

gravatar for msimmer92
msimmer92150
Reputation:
150
Status:
Trusted
Location:
Uruguay
Website:
https://www.linkedin.c...
Last seen:
3 weeks, 5 days ago
Joined:
2 years 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 • 68 results • page 1 of 7 • next >
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Comment: C: How to zoom out to whole genome view in UCSC browser?
... Ok, thank you very much! good to know ...
written 27 days ago by msimmer92150
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How to zoom out to whole genome view in UCSC browser?
... Hello, I have custom tracks with my ChIP-seq data on the UCSC browser. I created the bigWig files from the BAM files using deepTools' bamCoverage. I explored my files in IGV, IGB and UCSC browser. I would like to stick to the third one because has other nice functionalities, but I can´t seem to fi ...
ucsc bigwig browser written 27 days ago by msimmer92150 • updated 7 days ago by Luis Nassar60
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Comment: C: Can bedtools subtract support multiple files?
... Thank you for your answer! Yes, I had a typo in temp2.bed, I just edited it. The hyphen and paragraph dash thing might be because I wrote this on a Word document where I keep record of what I do and then copied from there and pasted it here.. sometimes when you copy and paste stuff to programs such ...
written 4 weeks ago by msimmer92150
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Can bedtools subtract support multiple files?
... I have four BED files with data from different conditions (let's say A B C and D). I want to make a file (using bedtools subtract) that have those regions specific to A. Since bedtools subtract works pairwise, I should do (manual example): bedtools subtract -a A.bed –b B.bed > temp1.bed ...
bedtools written 4 weeks ago by msimmer92150
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Comment: C: how to add bed files together
... Yes, you are right, you answered the users question properly because that question suggest finding the overlap. I just wanted to know for the union case and got confused reading the other answer. Let me rephrase ...
written 4 weeks ago by msimmer92150
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Comment: C: how to add bed files together
... This works wonderful, thank you. Just out of curiosity, is there an analogous of bedops -u in bedtools? (before someone answers bedtools intersect or merge, make sure that the options you include actually make the same output as bedops -u, because the default does not...please be more specific) ...
written 4 weeks ago by msimmer92150
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Comment: C: how to add bed files together
... Since we are discussing the bedtools intersect command: Is there a flag or something to add to bedtools intersect get the union, if I wanted to get it? ...
written 4 weeks ago by msimmer92150
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Comment: C: What is the difference between narrow peak, Broad peak and a gapped peak of a c
... I read that you could also call peaks in two runs, one with MACS2 narrow and another one with MACS2 broad, and then merge the output to have a mixed-type calling. Is this a correct way to do it, or is it better to call the mixed-type factors with other peak callers, such as PeakRanger's BCP, CCAT an ...
written 4 weeks ago by msimmer92150
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Comment: C: DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' lengt
... That is very kind of you to offer, thank you very much! I just shared with you the object. ...
written 4 weeks ago by msimmer92150
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Comment: C: MACS2 for K27me3 peak calling
... Very good idea to run it in both modes and then merge the results. Two questions: 1) would you recommend this for other histone marks as well (e.g. H4K5, H4K12)? 2) This post is from almost four years ago... does the new MACS2 have a mode to deal with mixed-type peaks data so that we don´t have to d ...
written 4 weeks ago by msimmer92150

Latest awards to msimmer92

Voter 7 weeks ago, voted more than 100 times.
Autobiographer 7 weeks ago, has more than 80 characters in the information field of the user's profile.
Supporter 10 months ago, voted at least 25 times.
Scholar 22 months ago, created an answer that has been accepted. For A: Error: --fst requires at least two nonempty clusters.

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