User: yasminsoareslima

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Posts by yasminsoareslima

<prev • 11 results • page 1 of 2 • next >
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Comment: C: SnPEff ANN[*].FEATURE and ANN[*].FEATUREID annotation
... Many thanks! Next time I'll do it right ...
written 3 months ago by yasminsoareslima10
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SnPEff ANN[*].FEATURE and ANN[*].FEATUREID annotation
... Hello everyone, I have a question regarding `ANN[*].FEATURE` and `ANN[*].FEATUREID` annotation from snpEff in case you know how to help me. I have variants in my annotated .tsv which comes with the following annotation for the `ANN[*].FEATURE` field: `structural_interaction_variant`. Then, for t ...
structural_interaction_variant snpeff written 3 months ago by yasminsoareslima10 • updated 3 months ago by RamRS23k
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Comment: C: IGV - identification of sequencing errors
... Yeah, they were supposed removed. ...
written 3 months ago by yasminsoareslima10
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Comment: C: IGV - identification of sequencing errors
... the calling was performed by Somatic variant caller, from Illumina. What are clipped bases? Primers and adaptors were supposed removed. Thank you ...
written 3 months ago by yasminsoareslima10
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IGV - identification of sequencing errors
... Hi to all, I've already read that Illumina reads mostly common present errors at the end.. however, never read about any issue at the beginning of them. I have called SNVs at the beginning and end of my reads that I don't feel like trusting, although the mapping quality and phread quality appears ...
snp sequencing written 3 months ago by yasminsoareslima10
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Comment: C: How to extract total allele frequency from gnomAD annotation
... Hi Manuel, Thank you for trying to help. yes, I downloaded my gnomAD file from gnomAD website. I haven't seen AF_adj for gnomAD either, it was just what I was expecting to find, as there is a field alike for ExAC for example. Thanks your comments I found the AF field and managed to annotate it. H ...
written 4 months ago by yasminsoareslima10
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Comment: C: How to extract total allele frequency from gnomAD annotation
... Hi Lecob, it is exactly what RamRS has said. I donwloaded the gnomAD VCF in order to use it to annotate MY vcf, with my data. And if you pay attention, this AF doesn't match with the AF described in the browser. The one would match with the browser it usually the adjusted one, i. e. AF_adj, but I c ...
written 4 months ago by yasminsoareslima10
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Comment: C: How to extract total allele frequency from gnomAD annotation
... yeah, but it seems I dont have the information "AF" in my vcf, that's why I'm wondering how it is being called or how it is annotated. Perhaps it comes with a different name, I don't know. ...
written 6 months ago by yasminsoareslima10
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How to extract total allele frequency from gnomAD annotation
... Hello people, I am quite confused about to extract the information I want from the Genomad annotation database (downloaded .vcf ). I've download the .vcf from Genomad and annotated using SnPEff, which resulted in maaany informations, for instance, the allele frequencies from each population, from c ...
allelefrequency af gnmoad written 6 months ago by yasminsoareslima10 • updated 4 months ago by lecob0
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Comment: C: HELP with variable assignment in bash loop for
... Thank you for the information and the kind response. No problems at all. Sorry, Yasmin ...
written 6 months ago by yasminsoareslima10

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