User: manuel.belmadani

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Posts by manuel.belmadani

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Comment: C: VEP not returning gnomAD AF
... You could try [wAnnovar][1] which seems to work for that variant. [1]: http://wannovar.wglab.org/ ...
written 9 months ago by manuel.belmadani1.2k
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Comment: C: how can i get p value from miRNA raw readcounts
... It really depend what's you're looking for, and what your data's like. Get an idea of what others have done first and what kind of tools they used, I find that's usually the best approach to figure it out. A good starting point would be to find some existing miRNA DE pipeline. Some links to get you ...
written 10 months ago by manuel.belmadani1.2k
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Comment: C: how can i get p value from miRNA raw readcounts
... You need to give us more information. A p-value is associated to a certain hypothesis/test. What are you testing here? What are you interested in knowing using the read counts? If you have multiple samples, you could compute a differential expression analysis where your miRNAs would have a p-value ...
written 10 months ago by manuel.belmadani1.2k
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Answer: A: How to get the list of common genes from a VennDiagram?
... From what I can tell, the `a`s are distributed from top left to right, to bottom. i.e. ``` a1 = 1761 a2=126 a3=466 a4=64 a5=44 a6=27 a7=366 ``` This is based on: ![enter image description here][1] > library("VennDiagram") > > gene_list = paste0("GENE", 1:1000) > ...
written 10 months ago by manuel.belmadani1.2k
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Comment: C: Download hundreds of genes' variant csv from gnomAD
... I don't think there's a single file with both (officially at least) but the exome variants are at https://storage.googleapis.com/gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz (link from the gnomAD download page: https://gnomad.broadinstitute.org/downloads). ...
written 10 months ago by manuel.belmadani1.2k
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Answer: A: How to write HGVS nomination for noncoding intergenic variants
... There's some documentation on: https://varnomen.hgvs.org/, specifically see here under non-coding variants: https://varnomen.hgvs.org/bg-material/refseq/ (see also: https://varnomen.hgvs.org/bg-material/consultation/svd-wg002/) Personally I usually handle it through some tool. You can do the conver ...
written 11 months ago by manuel.belmadani1.2k
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Comment: C: STAR or Bowtie for small RNA seq?
... Hi anara92; you might want to start your own question. There could be a lot of reasons why you're getting low mapping rates and often it doesn't even have to do with the parameters so you will get more precise help (and faster since it'll be asked to the whole Biostars community, not just people in ...
written 11 months ago by manuel.belmadani1.2k
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Comment: C: Download of FASTQ files from the European Nucleotide Archive (ENA) using Aspera
... > This leads to either two errors What are you doing differently to get the two errors? ...
written 12 months ago by manuel.belmadani1.2k
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Comment: C: Linear regression model
... Ok. Sounds like linear regression would be reasonable to look at. However there's a lot of different ways you could describe you model; are the variables [fixed or mixed effects][1] ? Are there interactions between variables? To start, you could just try a model where every variable is a fixed effe ...
written 12 months ago by manuel.belmadani1.2k
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Comment: C: Linear regression model
... Try to give a little bit more information. I'm assuming that column is age? To do linear regression, at the very least, you need two variables (Say, `X` and` Y`.) You want to predict `Y` based on inputs of `X`. Say here your age is your `X` variable, and you want to predict some other, dependent, ...
written 12 months ago by manuel.belmadani1.2k

Latest awards to manuel.belmadani

Teacher 10 months ago, created an answer with at least 3 up-votes. For A: NGS analysis: how to handle paired-end reads
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Scholar 15 months ago, created an answer that has been accepted. For A: wonderdump.sh and FTP site URL conventions for SRR identifiers
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