User: abhishek.abhishekkumar

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Germany
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Posts by abhishek.abhishekkumar

<prev • 7 results • page 1 of 1 • next >
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Answer: A: Looking for Training in opportunities in Bioinformatics?
... Two training programs are already mentioned above, I recommend you follow practical training sources: 1.Biostars handbook (https://www.biostarhandbook.com/) 2. Computational Exome and Genome Analysis Peter N. Robinson, Rosario Michael Piro, Marten Jager (https://www.crcpress.com/Computational-Ex ...
written 9 months ago by abhishek.abhishekkumar20
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Answer: A: model selection for MrBayes.
... Following criteria are used for selection of the best-fitting models: a) the Akaike Information Criterion (AIC), b) the Bayesian Information Criterion (BIC) and c) hierarchical Likelihood-ratio tests (hLRTs) Tools like 1. MEGA7 2.ModelGenerator (https://bmcevolbiol.biomedcentral.com/articles/10. ...
written 9 months ago by abhishek.abhishekkumar20
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Answer: A: Collaboration Request to Accomplish a Task
... its simple parshing of pdb file, several ways of doing this like a) GREP ****grep "GLY" test.pdb>output.pdb** **grep "CA" output.pdb>output2.pdb**** b) AWK You can do like based on your example in awk: **awk '$3 == "CA" {print $0}' test.pdb>output.pdb** and I assume you will wor ...
written 9 months ago by abhishek.abhishekkumar20
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Comment: A: how to find ratio of cases vs control per variant from a vcf file
... Thanks for the multiple answers - Pierre, as many of your ideas, worked for me in past, so special thanks. ...
written 19 months ago by abhishek.abhishekkumar20
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how to find ratio of cases vs control per variant from a vcf file
... how to find ratio of cases vs control per variant from a vcf file vcf file looks like - #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Co1 Co2 Ca1 Ca2 1 15455 . A C 2599 PASS AC=1;AF=6.227e-04;AN=1606;BaseQRankSum=-6.731e+00;CCC=1606;ClippingRankSum=1.27;DP=31258;FS=1.355;GQ_MEAN=99.94; ...
vcf case vs control written 19 months ago by abhishek.abhishekkumar20
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Answer: A: Awk or Shell script in need
... It is simple in awk: awk '{print $1, $2, $3, $4, $6, $7, $8, $10, $11, $12}' input_file>output_file Answer is valid only for the data provided initially like NC_007622|123-456 NC_234 123 568 NC_007622|123-456 NC_546 126 563 NC_007622|123-456 NC_564 582 369 than output will be:--> NC_0 ...
written 2.1 years ago by abhishek.abhishekkumar20
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Answer: A: How Do We Discourage Ad-Hoc Bioinformatic Analyses?
... Great question, it is all about objective of the project and long term goals of person handling the project. I agree that documentation is necessary. But there are several labs which just focus on their products they need, may be they will never repeat this experiment or these analyses again. PIs la ...
written 3.8 years ago by abhishek.abhishekkumar20

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