User: cocchi.e89

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cocchi.e8930
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Posts by cocchi.e89

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Comment: C: How to find the chromosomal coordinate of a mutation in a gene?
... @Pierre I tried to use back locate but when I run the example it gives me an error: echo -e "INF2\tA13T" | java -jar dist/backlocate.jar -R hg19.fa [WARN][BackLocate]ici [WARN][BackLocate]ici [INFO][BackLocate]loading genes [INFO][BackLocate]genes:99813 [INFO][BackLocate]loa ...
written 5 months ago by cocchi.e8930
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Retrieve base position/coordinates due to AA position on a protein
... I'm trying to understand at which nucleic bases would correspond the DID-domain of INF2 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2980844/). As example, they say that all mutations are found between AA 13 and 220 (Table 1 of publication linked). How can I retrieve the genetic coordinates of base ...
base coordinates position aminoacid written 5 months ago by cocchi.e8930
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Comment: C: UCSC different exome sets per each gene
... Found a good answer finally at: https://www.biostars.org/p/93011/ ...
written 6 months ago by cocchi.e8930
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Comment: C: UCSC different exome sets per each gene
... if I leave "UCSC Genes" in the query page it doesn't allow me to select "Coding Exons" in the BED page, but if I change it to "NCBI RefSeq" it then does and I get: chr1 67000041 67000051 NM_001308203.1_cds_1_0_chr1_67000042_f 0 + chr1 67091529 67091593 NM_001308203.1_cds_2_0_chr1_67091530_f ...
written 6 months ago by cocchi.e8930
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Comment: C: UCSC different exome sets per each gene
... Thank you very much for the suggestions Luis, but I need the start-end of each exome, not of the overall gene. ...
written 6 months ago by cocchi.e8930
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Comment: C: UCSC different exome sets per each gene
... probably the largest, shall I calculate it for each one? Or there is a sort of "indicator" of the largest set? ...
written 6 months ago by cocchi.e8930
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UCSC different exome sets per each gene
... I'm trying to collect the exomes' start-end for a set of gene. I downloaded the UCSC tables, but I found out that different sets are outputted for each gene. As example UMOD gene: #hg19.knownGene.name hg19.knownGene.chrom hg19.knownGene.txStart hg19.knownGene.txEnd hg19.knownGene.exonCount hg19 ...
gene coordinates exomes ucsc written 6 months ago by cocchi.e8930 • updated 6 months ago by Luis Nassar180
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Comment: C: InterVar and Varsome discrepancies in ACMG classification
... Just clone the InterVar repo on GitHub: git clone https://github.com/WGLab/InterVar.git and then access the InterVar directory in which you find the python script InterVar.py Call it on a normal VCF file with, as example (I use python3.7 but any distribution >3.3 should work properly): ...
written 6 months ago by cocchi.e8930
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InterVar and Varsome discrepancies in ACMG classification
... I am working on ACMG classification of variants in a cohort of patients, I found that InterVar classification differs (generally more strict for what does it seems to me at the moment) form Varsome, e.g. var X-107939570-C-T is classified as "*Pathogenic*" by Varsome (https://varsome.com/variant/hg19 ...
guidelines intervar varsome acmg written 6 months ago by cocchi.e8930 • updated 5 months ago by manuel.belmadani1.1k
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Comment: C: hom/het definition from Allelic Depth counts
... Thanks for your reply! Data is from WGS ...
written 7 months ago by cocchi.e8930

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