User: caspase8mach

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caspase8mach10
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Posts by caspase8mach

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
... Thanks a lot Kevin for the prompt reply. How can I extract only the genotypes from various vcf files I have, extract common variants and merge those? I want to create a merged VCF file from various individual vcf files, similar to the 1000 Genomes merged VCF file. ...
written 8 months ago by caspase8mach10
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Comment: A: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
... Hello Kevin, Thanks for the wonderful tutorial. I have one basic question, and I will really appreciate help from your side. I have multiple vcf files. How can I merge those to create a 'mega' vcf file (vcf matrix file) having only the genotype information, to be used along with the 'merged' VCF f ...
written 8 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Certainly helpful, will give it a try and let you know. Any one with an experience with the Apache Spark based DNA NGS Pipeline(s)? Thanks ...
written 19 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Thanks a lot. As suggested, I created index file using ``` bwa index hg19.fasta ``` and got the following files: ``` hg19.fasta hg19.fasta.amb hg19.fasta.ann hg19.fasta.bwt hg19.fasta.pac hg19.fasta.sa ``` I did manage to align a pair of FastQ files using **your Snakemake tutorial**, hurray ... m ...
written 19 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Awesome, thanks a lot for the link to the nice tutorial! Its great! What index file do you mean? > What index file do you mean? For mapping the Fastq file using a reference genome, do I need to create an index first? Thanks a lot. ...
written 19 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Thanks a lot for the information. Am going through the suggested resources to learn and build a genomics pipeline(s). Thanks a lot. ...
written 19 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Thanks finswimmer for the workflow ... certainly will help me to learn. By any chance do you have links for the .fa and multiple fastq files for me to give this example a try? Do I also have to provide an index file? TIA ...
written 19 months ago by caspase8mach10
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Comment: C: Genomics (DNA) Pipeline - Example
... Thanks for the info, but somehow I am not able to access the URL you wrote/suggested. Could you please give me the correct URL? Thanks ...
written 19 months ago by caspase8mach10
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Genomics (DNA) Pipeline - Example
... Hello all, Is there a good example of a genomics pipeline ready to be used for mapping/alignment of NGS data (preferably whole genome) followed by variant calling / annotation along with generation / visualization of quality matrices? It will be even better if the suggested pipeline is Python based ...
variant calling annotation alignment python written 19 months ago by caspase8mach10
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DNA Methylation Analysis
... Hello All, I am in the process of analyzing huge DNA methylation data and your help on this will be very helpful. I have various .txt files, each file having 1 column and approx 450K rows representing 450K CpGs which are either methylated or not. What kind of tools / scripts / resources (R/Python ...
dna methylation ngs matrix R python written 2.5 years ago by caspase8mach10

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