User: Dhana

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Dhana60
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Helsinki, Finland
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3 years, 7 months ago
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Bioinformatics master student.

Posts by Dhana

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Create linkage disequilibrium file
... Thank you Tokhir. The solution you suggested worked for generating the file but on the other hand the generated file is so huge that it cannot be uploaded in locus explorer. For my original file, containing about 34 SNPs the generated LD file was around 50 Mb (559621 LD values), to cross verify it I ...
written 8 days ago by Dhana60
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Comment: C: Create linkage disequilibrium file
... Hi, thank you for your reply. I tried the [--biallelic-only strict][1] flag as well, still the same error message. The data is not my own so I am not at liberty to share it publicly. I have given a sample of the SNP file below; > snplist.txt > >rs148170422 > >rs547289895 > >r ...
written 9 days ago by Dhana60
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Create linkage disequilibrium file
... Hi, I am trying to calculate linkage disequilibrium (LD) values for a group of SNPs to be used as an input for the tool [Locus explorer][1] . I followed the tutorial they had mentioned in their help section to [create LD file][2] from 1000 Genomes data, When I try to replicate their example ( examp ...
locusexplorer snp linkage disequilibrium plink ld written 9 days ago by Dhana60 • updated 8 days ago by zx87544.3k
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Answer: A: NGS CNV tools for windows users
... If you are really interested in bioinformatics then you MUST start using UNIX based OS, most tools nowadays are developed to be run in command line (as it can be integrated into a pipeline easily). Few options for windows OS would be: 1. Install [virtual machine][1] and then download [Biolinux][2] ...
written 14 months ago by Dhana60
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Comment: C: SnpMatrix from VCF file
... > var snp_id=0; > var samples = header.getSampleNamesInOrder(); > out.print("id"); > for(var i=0;i< samples.size();++i) > { > out.print("\t"+samples.get(i)); > } > out.println(); > > while(iter.hasNext()) { > ...
written 14 months ago by Dhana60
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Comment: C: SnpMatrix from VCF file
... Hi [Pierre][1], I used the Bioalcidae tool and the provided script for generating the matrix, I wanted to ask is it possible to replace the first field (ID's) of the resulting matrix to the respective variant ID's from the vcf file? or is using the tools such as cut or awk to replace the ids is the ...
written 14 months ago by Dhana60
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Comment: C: SnpMatrix from VCF file
... Thank you very much [Pierre][1]. This was the solution I was looking for. [1]: https://www.biostars.org/u/30/ ...
written 14 months ago by Dhana60
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SnpMatrix from VCF file
... Hi, I am planning on doing eQTL analysis using the MatrixEQTL R ([MatrixEQTL link][1]) package and I need to extract genotype information and create a SnpMatrix file for that like the one given here [SNP.txt file link][2]. I have tried vcftools to create a similar looking file but to no avail, I ha ...
vcf matrixeqtl snpmatrix vcftools eqtl written 14 months ago by Dhana60 • updated 11 weeks ago by Leandro Lima890
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Comment: C: Complete Genomics data analysis, pipeline version and batch effect
... Yes the join tool takes only two files as input. But that does not limit its uses, since the tool is able to read input from stdin and pass output to stdout. You can write a loop in bash/python for it to merge all the files. ...
written 2.5 years ago by Dhana60
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Answer: A: Complete Genomics data analysis, pipeline version and batch effect
... For the annotation part, you can use cgatools join command. Since the data is also from Complete Genomics Inc. it will be easier to use cgatools for most part. You can use it as; cgatools join --beta --input <file1> <file2> \ –-match <specifications> \ --overlap <specifica ...
written 2.5 years ago by Dhana60

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Popular Question 8 months ago, created a question with more than 1,000 views. For SnpMatrix from VCF file

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