User: sofie_carolina

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Hyderabad
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3 weeks, 1 day ago
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1 year, 9 months ago
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Posts by sofie_carolina

<prev • 40 results • page 1 of 4 • next >
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Compare two cols of one file to another file of same cols and fetch the matches
... I have file1 of 6.5lakh rows with two cols, "Chr" and "Pos". I want to compare this file with dbsnp (file2) datadump and match with with Chr and Pos col present in dbSNP dump. Once matched, respective rsid's to be fetched. I tried using Python Panda's but my process is getting killed. When it tried ...
genome gene next-gen snp python written 6 weeks ago by sofie_carolina20
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(Closed) Basic difference between haplotype variant callers
... What is the basic difference between variant callers (haplotype calling). We have callers like, GATK, Freebayes, Vardict, Platypus, etc. Each callers have their own sensitivity to call variants as per to mapped reads. What more basic difference they have ? For fetching all the variants (possibly) wh ...
genome gatk next-gen snp sequencing written 6 weeks ago by sofie_carolina20
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Comment: C: PRSice polygenic score with only controls
... Hi, Even I am also getting same error. But, after giving phenotype file, this is the error now, Error in family$linkfun(mustart) : Argument mu must be a nonempty numeric vector Calls: summary ... glm -> eval -> eval -> glm.fit -> -> .Call Execution halted ...
written 9 weeks ago by sofie_carolina20
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Polygenic Risk Score analysis using PRSice
... I am doing Polygenic Risk Score analysis for microarray data with a specific trait. I am facing problem to understand the outputs generated by PRSice application (v1.25) and looking forward for any guidance or help for the same. Questions are: 1. How to set individual PRS quantile (specific traits ...
genome gwas next-gen snp sequencing written 10 weeks ago by sofie_carolina20
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Comment: C: What is REF and ALT ? Does all variations are mutations ?
... Thanks for your kind consideration. I will perform the analysis as you have suggested. My query was just to confirm what is difference between variation and mutation. I too also have some more doubts :), If you are kind enough I can ask. One more doubt I have. Do we need to use mutation thresholds ...
written 10 weeks ago by sofie_carolina20
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Comment: C: How to download SNPedia database or data dump
... Yes, I have seen that and also downloaded but max 500 hits are possible I guess ? Also, I am not getting magnitude information in the downloaded cols of SNPedia. ...
written 10 weeks ago by sofie_carolina20
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Comment: C: What is REF and ALT ? Does all variations are mutations ?
... It's Ok Mam. Thank you for your honest help. I respect your generosity. Being a researcher, I do also help to many of my colleagues and juniors. I asked this question just to clarify how bioinformaticians narrate difference between mutation and variation. Please don't misunderstand me. Thanks a lot ...
written 10 weeks ago by sofie_carolina20
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Comment: C: What is REF and ALT ? Does all variations are mutations ?
... Sorry for the inconvenience. I kept these things confidential as per policies of my institute. Please understand. I apologize for the same. ...
written 10 weeks ago by sofie_carolina20
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Comment: C: What is REF and ALT ? Does all variations are mutations ?
... SNPS Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene cytoBand SIFT_score SIFT_pred Polyphen2_HDIV_score Polyphen2_HDIV_pred Polyphen2_HVAR_score Polyphen2_HVAR_pred LRT_score LRT_pred MutationTaster_score MutationTaster_pred MutationAssessor ...
written 10 weeks ago by sofie_carolina20 • updated 10 weeks ago by Emily_Ensembl18k
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Comment: C: What is REF and ALT ? Does all variations are mutations ?
... No, I have given the input of all the variants (~6lkhs) as vcf to ANNOVAR. The case that I shared is for one single variant having snpid, chr, pos, ref, alt and other annotation scores as annotated from Annovar. ...
written 10 weeks ago by sofie_carolina20

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