User: roalva1

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roalva180
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Posts by roalva1

<prev • 36 results • page 1 of 4 • next >
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Comment: C: bcftools expression string exact match
... Yes it seems so, also I execute this: bcftools query -i "CLNSIG='Pathogenic'" -f '%CLNSIG\n' clinvar.vcf.gz | sort -u The result is Pathogenic Pathogenic,_Affects Pathogenic,_association Pathogenic,_association,_protective Pathogenic,_drug_response Pathogenic,_drug_response,_other Pathogenic,_ ...
written 10 months ago by roalva180
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bcftools expression string exact match
... Hello, If I execute this in bcftools 1.10.2 clinvar.vcf.gz is https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz bcftools query -i "CLNREVSTAT='criteria_provided,_conflicting_interpretations'" -f '%CLNREVSTAT\n' clinvar.vcf.gz | sort -u I get this results: criteria_provided,_co ...
bcftools written 10 months ago by roalva180
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Differences in HGVS notation
... Hello, I am trying to understand why these two variants are not the same: - NM_153818.1:c.927_928insG: varso.me/L2FR - NM_153818.1:c.926_927insG: varso.me/L22e by HGVS notation and the 5'->3' arrange, I think they should be the same. Normally, Varsome would change the second to the first but i ...
hgvs varsome written 15 months ago by roalva180 • updated 15 months ago by finswimmer14k
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Comment: C: Enrichment analisys with clusterProfiler in CNVs
... Thanks a lot for the answer. On the other hand, would be correct to mix deleted and amplified genes? or better do them separately? I was thinking in the biological sense. ...
written 16 months ago by roalva180
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Enrichment analisys with clusterProfiler in CNVs
... Hello, is it possible to use clusterProfiler for CNVs?or is it only for differential expressed genes or chipseq? Thanks! ...
enrichment clusterprofiler cnv written 16 months ago by roalva180 • updated 16 months ago by jared.andrews078.6k
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Classify benign tumor vs malign tumor
... Hello, I am using the Trusight Tumor 170 kit from Illumina. I have sequenced 10 benign tumor samples and 10 malign tumos samples. I would like to create a classifier based on snps and indels (what Illumina calls small variants). I have already some snps and indels that belongs only to the malign s ...
indels snps tumor written 2.6 years ago by roalva180
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Comment: C: nonamecheck not working in bedtools coverage
... Yes, I don't have any chrM regions in my bed file, but I do have in my bam. The message of bedtools should be a warning but it is not. Bedtools stops and the coverage in chrX regions are not calculated. ...
written 2.7 years ago by roalva180
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Comment: C: nonamecheck not working in bedtools coverage
... My bed file doesn't have any region in chrMT nor chrM ...
written 2.7 years ago by roalva180
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Comment: C: nonamecheck not working in bedtools coverage
... No no, I have got just a bam ...
written 2.7 years ago by roalva180
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Comment: C: nonamecheck not working in bedtools coverage
... This has solved my problem, but still, with bedtools 2.17 we didn't need this, and I think it is not intuitive. ...
written 2.7 years ago by roalva180

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