User: manuel.belmadani

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Posts by manuel.belmadani

<prev • 117 results • page 1 of 12 • next >
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Answer: A: VCF File type
... That group is called the "genotype", and yes, you could have `2` or higher if there's 2 or more non-reference alleles, and you can have a pipe `|` instead of `/` if the genotype is phased. > GT genotype, encoded as alleles values separated by either of ”/” or > “|”, e.g. The allele values are ...
written 17 hours ago by manuel.belmadani980
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Answer: A: RNA-Seq: Getting Started with Kallisto
... Your reads would be in FASTQ format, not FASTA, though you will possibly have a transcriptome/genome reference in FASTA format. A typical workflow I would say is something like: - Start with by getting some FASTQ files, have them in separate directories per sample (this is something that's done e ...
written 11 days ago by manuel.belmadani980
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Comment: C: Reproducing normalized values from raw data in GSE20346
... Maybe this isn't exactly what you're looking for but, but GSE20346 has been re-processed and analyzed on our Gemma database: - Experiment page: https://gemma.msl.ubc.ca/expressionExperiment/showExpressionExperiment.html?id=3023 - Controls are shown here: https://gemma.msl.ubc.ca/experimentalDesig ...
written 12 days ago by manuel.belmadani980
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Answer: A: InterVar and Varsome discrepancies in ACMG classification
... You can actually replicate what InterVar tells you with the VarSome UI. Example: PVS1=0 PS=[0, 0, 0, 0, 0] PM=[0, 1, 0, 0, 0, 0, 0] PP=[0, 0, 1, 0, 1, 0] BA1=0 BS=[0, 0, 0, 0, 0] BP=[1, 0, 0, 0, 0, 0, 0, 0] ![enter image description here][1] Why do they get different information? I'm not too fam ...
written 13 days ago by manuel.belmadani980
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Answer: C: Novel peptide identification
... Do you mean that you have 30,000 distinct peptides that you want to search or you have one (or more) peptides of length 30,000 (i.e. 30,000 characters long)? I think you probably mean 30,000 peptides, and I assume your peptides are probably pretty short, i.e. as short as 2 amino acids to dozens, ...
written 19 days ago by manuel.belmadani980
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Comment: C: Wrong results in differential gene expression analysis
... Did you try running the script they provided? https://github.com/akram-mohammed/septic_shock_degs/blob/master/sepsisGenomics_DGE.R ...
written 4 weeks ago by manuel.belmadani980
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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... Can you plot and show the distribution of p-values for your genes? Is it flat? ...
written 5 weeks ago by manuel.belmadani980
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Comment: C: All result in one file
... Which one? Does it give you an error message or it doesn't merge them properly? The main problem I see is that you're getting `res` from biomart. So calling `res[[k]]` doesn't seem to make sense since biomart doesn't know that you have `k` files, that's why I assumed you were using `i` in `res[[i]] ...
written 5 weeks ago by manuel.belmadani980
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Answer: A: All result in one file
... The easiest way to fix that would be to change your filename as you're writing is, for example: write.csv(res[[i]], file = paste0("recovery_gene_trans_",k,".txt")) So for each `k` file, your file name with be suffixed with `k.txt`. But what is `i` here? it shows up in your `write.csv` but do ...
written 5 weeks ago by manuel.belmadani980 • updated 5 weeks ago by zx87547.8k
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Answer: A: How to obtain transcript level TPM using stringtie?
... It does provide transcript level TPM since 2015: > 10/19/2015 - v1.1.0 release This StringTie release includes the > following updates: major memory usage improvements due to: changes of > internal data structures, collapsing reads aligned in the same place > and filtering of spurious s ...
written 6 weeks ago by manuel.belmadani980

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