User: vguerracanedo

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Posts by vguerracanedo

<prev • 6 results • page 1 of 1 • next >
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DiscoSNP++ downstream analysis + multiple SNP question
... Hi Everyone, I have a few genes of interest from a de novo RNA-seq library assembly that I would like to phase (variant call). I don't have a genome to use. For one of my genes (~10,000bp long), I did a pairwise analysis (Blast) and I get ~100 IDs for SNPs when I filter for rank values higher t ...
discosnp discnosnp++ rna-seq written 6 months ago by vguerracanedo10
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Using the ranking value to filter
... Hi there, I'm working on trying to create a filter for the low quality SNPs of my data, and I thought of basing the filter on the ranking values (https://www.biorxiv.org/content/early/2017/10/27/209965). I lose ~99% of my SNPs when I only look at the SNPs with ranking higher than 0.2. This filte ...
discosnp++ discosnp rna-seq variantcalling filter written 6 months ago by vguerracanedo10 • updated 6 months ago by pierre.peterlongo830
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Comment: C: kissplice2reftranscriptome interpreting output
... Hi Vincent, I'm also having a hard time interpreting the output. I was wondering if you could give me a hand. When the snp change is in the second position of the codon, then we can predict that the codon of interest is in the middle of the 5 nucleotides that you mentioned. But how can we find t ...
written 7 months ago by vguerracanedo10
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Kissplice2RefTranscriptome interpreting results
... Hi Everyone, I was looking at my results from Kissplice2RefTranscriptome and I note that SNPs were annotated for my mitochondrial genes. This doesn't look right because the mitochondrial genes of my organism are haploid. I followed the steps as noted in the manual with a Trinity De novo assembly. ...
rna-seq written 22 months ago by vguerracanedo10
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Answer: A: Problems installing kissplice2reftranscriptome
... Ha! The team at Westgrid gave me the quick solution: add the word 'python' before the command. ...
written 22 months ago by vguerracanedo10
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Problems installing kissplice2reftranscriptome
... Dear all, I'm getting the following error 'Permission denied' when I try to run kissplice2reftranscriptome after the installation. Does anyone have an idea of what I should do to fix it? Best, Vanessa ...
rna-seq written 22 months ago by vguerracanedo10

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