User: msimmer92
msimmer92 • 260
- Reputation:
- 260
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- Trusted
- Location:
- Uruguay
- Website:
- https://www.linkedin.c...
- Last seen:
- 7 months, 3 weeks ago
- Joined:
- 3 years, 9 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
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... Does anyone know how to translate the Gene Set names from msigdb (e.g. GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION) to their GO IDs (e.g. GO:0050434) in R ?
Is there a table somewhere I could use to do the conversion? Or some package?
Thank you! ...
written 7 months ago by
msimmer92 • 260
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... Yes (but I also tried without them and the error persists). The thing is, at first I tried to put inside the variable exactly the same string I have in the first script. It didn't work. I thought "maybe I think it's getting passed in the same way, but in practice it is not?". Thus, I started experim ...
written 9 months ago by
msimmer92 • 260
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... I am practicing Snakemake. Wanted to make a MACS2 callpeak code, and ran into problems when I wanted to add a level of complexity (from making a simple code for the basic, narrow peak case, to trying to make one that is flexible to both broad and narrow scenarios). First, I did the following (basic ...
written 9 months ago by
msimmer92 • 260
• updated
8 months ago by
Jeremy Leipzig ♦ 19k
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... Dmitry Kuzminov solved it in StackOverflow. I share the answer here, in case someone has the same doubt!
It seems there is an extra parenthesis at the end of the "input" line in the samtools_dup rule. I honestly didn't spot it, and also the error message made me think the problem wasn't there but a ...
written 10 months ago by
msimmer92 • 260
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... There is an empty line (two enters, from the end of the shell line) and then what you see in the second code panel (the bigwig rule - I added it now to this question). When I delete the samtools_dup rule, the code works. I'll try to put it again and double-check indentations, but the next rule's fir ...
written 10 months ago by
msimmer92 • 260
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... There is some problem with my samtools_dup rule.
It says **"SyntaxError in line 201 of /data/mypipeline.smk: No rule keywords allowed after run/shell/script/wrapper/cwl in rule samtools_dup. (mypipeline.smk, line 201)"**.
If I google the error, I found that a person says that, in their code, might ...
written 10 months ago by
msimmer92 • 260
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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 12 months ago by
msimmer92 • 260
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... not from my side. still same problem ...
written 14 months ago by
msimmer92 • 260
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... Ok, thank you, both! I'll check out those papers. ...
written 14 months ago by
msimmer92 • 260
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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 14 months ago by
msimmer92 • 260
• updated
14 months ago by
jared.andrews07 ♦ 8.3k
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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 A: Error: --fst requires at least two nonempty clusters.
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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 The 2013 Eisenberg and Levanon housekeeping genes list for Human is the most updated one?
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