User: Dhana

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Dhana70
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Helsinki, Finland
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Bioinformatics master student.

Posts by Dhana

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Installing samtools from sourceforge
... The samtools executable should be located with the bin folder. It should run when you run it as `/bin/samtools` ...
written 1 day ago by Dhana70
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Answer: A: how to detect association between SNP and expression?
... It is still possible to do eQTL analysis with 18 samples, you can try using the [Matrix eQTL][1] package. I have used it previously and found it to be very simple and efficient. In case you do not find any eQTLs in it might be good to try other non-parametric tests such as Kruskal-Wallis and plot th ...
written 6 days ago by Dhana70
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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 5 months ago by Dhana70
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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 5 months ago by Dhana70
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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 5 months ago by Dhana70 • updated 5 months ago by zx87545.3k
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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 18 months ago by Dhana70
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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 19 months ago by Dhana70
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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 19 months ago by Dhana70
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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 19 months ago by Dhana70
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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 19 months ago by Dhana70 • updated 7 months ago by Leandro Lima900

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Popular Question 13 months ago, created a question with more than 1,000 views. For SnpMatrix from VCF file

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