User: svp

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svp240
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Bangalore
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snijesh
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Posts by svp

<prev • 40 results • page 1 of 4 • next >
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Comment: C: Access metadata in GEO expression datasets
... Can you post the code that you have tried to access the file? ...
written 2 days ago by svp240
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Comment: C: Color code samples
... Can you make the question more clear? ...
written 25 days ago by svp240
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Comment: C: Deseq2 : Error some values in assay are not integers
... You can follow [this][1] [1]: https://www.biostars.org/p/368158/ ...
written 28 days ago by svp240
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Comment: C: SNPs not filtered from a GATK vcf file
... You can also use `SelectVariants` module from GATK ...
written 6 weeks ago by svp240
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Answer: A: Web scraping in the KEGG db
... You can try using TOGOWS get the genes for Alzheimer disease: hsa05010 as JSON http://togows.dbcls.jp/entry/pathway/hsa05010/genes.json [ { "102": "ADAM10; ADAM metallopeptidase domain 10 [KO:K06704] [EC:3.4.24.81]", "6868": "ADAM17; ADAM metallopeptidase domain 17 [KO ...
written 6 weeks ago by svp240
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Answer: A: RSEM Error - rsem-calculate-expression
... There is an error in the command used. You should use the index name correctly. In the following command `mouse_ref` is reference index name which should used in `rsem-calculate-expression` also. ###For preparing the reference rsem-prepare-reference --gtf ref/Mus_musculus.GRCm38.99.gtf --bowt ...
written 7 weeks ago by svp240
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How to classify Tumor Mutation Burden into TMB high, medium and low groups ?
... Tumor mutational burden (TMB) is a measure of the number of gene mutations inside the cancer cells. TMB of a tumor sample is calculated by the number of non-synonymous somatic mutations per mega-base in coding regions. The value obtained for TMB always ranges from 0 to 1 which never reaches 1. What ...
exome tumor mutation burden tmb written 7 weeks ago by svp240 • updated 7 weeks ago by Karma300
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Does HaploypeCaller detects somatic mutations also?
... I know that HaplotypeCaller is designed to call germline variants which is different from the reference genome. Knowing the fact that somatic mutations are also different from the reference genome HaplotypeCaller picks these variations into account. Hence, the variants called by HaplotypeCaller cont ...
haplotypecaller exome mutation somatic germline written 10 weeks ago by svp240 • updated 10 weeks ago by WouterDeCoster44k
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what is the difference between calling variants with and without interval list?
... I used following command ##With interval list ###Step1 gatk HaplotypeCaller --input $sample.bqsr.bam --reference $reference --emit-ref-confidence GVCF --dbsnp $DBSNP --output $sample._genome.vcf.gz -L $interval ###Step2 gatk GenotypeGVCFs -R $reference --variant $sample._genome.vcf.gz -O ...
haplotypecaller gatk intervallist written 10 weeks ago by svp240 • updated 10 weeks ago by ekwame60
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How to interpret the values given in the BisoGenet output table ?
... I used Cytoscape App BisoGenet plugin to generate protein-protein interaction network. The annotation table of provided by BisoGenet contain column ' **bg.annotation.ExperimMethods**' which explains about the method for interaction evidence. But I am not sure about the values 1, 93, 81, 80 , 47... e ...
bisogenet protein interction nework cytoscape written 10 weeks ago by svp240 • updated 10 weeks ago by scooter380

Latest awards to svp

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Web scraping in the KEGG db
Supporter 3 months ago, voted at least 25 times.

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