User: msimmer92
msimmer92 • 150
- 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
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... Ok, thank you very much! good to know ...
written 27 days ago by
msimmer92 • 150
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... 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 ...
written 27 days ago by
msimmer92 • 150
• updated
7 days ago by
Luis Nassar • 60
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... 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
msimmer92 • 150
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... 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
...
written 4 weeks ago by
msimmer92 • 150
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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
msimmer92 • 150
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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
msimmer92 • 150
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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
msimmer92 • 150
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... 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
msimmer92 • 150
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... That is very kind of you to offer, thank you very much! I just shared with you the object. ...
written 4 weeks ago by
msimmer92 • 150
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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
msimmer92 • 150
Latest awards to msimmer92
Voter
7 weeks ago,
voted more than 100 times.
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7 weeks ago,
has more than 80 characters in the information field of the user's profile.
Student
9 weeks ago,
asked a question with at least 3 up-votes.
For The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
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10 months ago,
voted at least 25 times.
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Subsetting individuals with Plink. Error: Line 1 of --keep file has fewer tokens than expected
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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