User: msimmer92

gravatar for msimmer92
msimmer92260
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

<prev • 95 results • page 1 of 10 • next >
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Converting Gene Set names from msigbd to their GO (Gene Ontology) IDs
... 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! ...
msigdb R terms go ontology written 7 months ago by msimmer92260
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Comment: C: Generalizing snakemake MACS2 code - WildcardError Wildcards in input files canno
... 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 msimmer92260
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Generalizing snakemake MACS2 code - WildcardError Wildcards in input files cannot be determined from output files: 'sample'
... 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 ...
snakemake written 9 months ago by msimmer92260 • updated 8 months ago by Jeremy Leipzig19k
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Answer: A: Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/c
... 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 msimmer92260
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Comment: C: Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/c
... 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 msimmer92260
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Snakemake SyntaxError: No rule keywords allowed after run/shell/script/wrapper/cwl in rule
... 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 ...
rule snakemake syntaxerror keywords written 10 months ago by msimmer92260
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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 12 months ago by msimmer92260
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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 14 months ago by msimmer92260
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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 14 months ago by msimmer92260
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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 14 months ago by msimmer92260 • updated 14 months ago by jared.andrews078.3k

Latest awards to msimmer92

Scholar 10 months ago, created an answer that has been accepted. For A: Error: --fst requires at least two nonempty clusters.
Voter 23 months ago, voted more than 100 times.
Autobiographer 23 months ago, has more than 80 characters in the information field of the user's profile.
Supporter 2.7 years ago, voted at least 25 times.
Scholar 3.6 years ago, created an answer that has been accepted. For A: Error: --fst requires at least two nonempty clusters.

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