User: User 1933

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User 1933340
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6 years, 6 months ago
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9 years, 6 months ago
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Posts by User 1933

<prev • 83 results • page 2 of 9 • next >
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Comment: C: 1000 Variant Calling Parameters
... My goal is to show the level of strength of our variants. I am told, reporting the frequency of the variant in 1Kg is not enough. I am thinking about a new strategy, such as runing the 1KG pipeline by myself and doing a 1-1 comparison. I appreciate any suggestion. ...
written 6.8 years ago by User 1933340
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Comment: C: 1000 Variant Calling Parameters
... thanks - so how one can use 1000g to compare the significance of finding some variation in another cohort ?! Only based on the frequency of the variance ?! ...
written 6.9 years ago by User 1933340
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1000 Variant Calling Parameters
... I am sure not if I should ask this question here ! but I hope to get an answer. Before asking my question I read here http://www.1000genomes.org/analysis but couldn't find my answer. I wonder, with what setting the variant calling has been done in the 1000 genomes project. by setting, I mean, the mi ...
1000genomes gatk written 6.9 years ago by User 1933340 • updated 6.9 years ago by zam.iqbal.genome1.7k
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Comment: C: Length Of The Longest Available Cdnas For Gene Set
... if I want to do this analysis in the genome scale - from where I can download all transcripts ? thanks ...
written 6.9 years ago by User 1933340
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Comment: C: Length Of The Longest Available Cdnas For Gene Set
... thanks - can you elaborate how can I do it by having a HGNC id. I can get genomics coordinate from them. but I am not sure how to proceed ...
written 6.9 years ago by User 1933340
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Length Of The Longest Available Cdnas For Gene Set
... I would like to know what are the cDNA lengths for a gene set. for example, for 1 gene, I can go to ensembl.org and type LRP2 and see the longest length is 15808bp. I was wondering, if there is any R library / Python module / SQL query that I can use for ? Also as a side question, does CDS Length e ...
written 6.9 years ago by User 1933340 • updated 6.9 years ago by Istvan Albert ♦♦ 85k
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Answer: A: How Can I Create Similarity Matrix From Gene Expression And Rnaseq Data?
... You need to measure the similarity. There are different methods, such as correlation, information theory and a other kernel methods. for example in R let say you have a dataset like this dt = replicate(3, rnorm(4)) there are bunch of kernel functions in the kernlab library say we want to measu ...
written 6.9 years ago by User 1933340
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Comment: C: Variant Effect And The Impact Of Samples
... Thanks for explaining about the protein-affecting variants. I have added some more code to explain why do I mean ...
written 6.9 years ago by User 1933340
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Variant Effect And The Impact Of Samples
... I have extracted a region from 1KG webserver like mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -N -e 'select concat("ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20110521/ALL.",K.chrom,".phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz"),concat(RIGHT(K.chrom, ...
written 6.9 years ago by User 1933340 • updated 6.9 years ago by Emily_Ensembl21k
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Answer: A: Is There An Easy Way Of Getting Gene Symbols From Genomic Coordinates?
... if you list your region like 1:9330001:9395000 1:149242001:149250000 1:171936001:171971000 1:174059001:174143000 1:219914001:227775000 you can use the following code to get the corresponding gene symbols. rm(list = ls()) your_region = read.table("yourtable.csv") library("biomaRt") ensembl = use ...
written 6.9 years ago by User 1933340

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