User: preetipankajakshanpillai

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Posts by preetipankajakshanpillai

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(Closed) Missing IntervalFile.R in PureCN
... Hello to all, I am working with whole genome sequence data to call copy number variant. I want to use purity and ploidy aware copy number caller, so, I chose PureCN for this. I downloaded the PureCN package from the official website. Now to start working with my data, I need to generate a basic int ...
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Answer: A: RefSeq Annotation using SnpEff
... Hello all, I found the solution for the above. I downloaded the complete set of genes and their RefSeq IDs from UCSC website in text format. Copied whole genome sequence (reference), in fasta format, to the same folder. Edited my existing human database (GRCh38) in SnpEff using the following comman ...
written 3 months ago by preetipankajakshanpillai0
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RefSeq Annotation using SnpEff
... Hello, I am working with human whole genome sequence. I have called variant using samtools and I have annotated my VCF file using SnpEff. In the resultant file I have got only the Ensembl gene and transcript IDs. According to SnpEff documentations, SnpEff supports RefSeq as well, but I am not getti ...
snpeff ngs snp written 3 months ago by preetipankajakshanpillai0
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Add RefSeq ID to VCF file
... Hello! I am working with whole genome sequence of homo sapiens. I aligned my sample data with hg38, generated VCF file and finally annotated using bwa, samtools and snpeff, respectively. The final VCF file after snpeff annotation contains ensembl IDs in the information region. I want to incorporate ...
annotation ngs written 3 months ago by preetipankajakshanpillai0
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Picard:command not found
... I am working with Galaxy local instance on CentOS. I have installed Picard (owner devteam and revision 6741a8ace658) from ToolShed. It has installed properly but I am not able to use the tools. While running its throwing error "**Fatal error: Exit code 127 () /home/preeti/Galaxy/galaxy-dist/database ...
picard galaxy software error written 3 months ago by preetipankajakshanpillai0 • updated 3 months ago by Jennifer Hillman Jackson22k
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Answer: A: Error while installing ncurses 5.9
... Hello Wolfgang! I am working with CentOS 7. I installed Patch to the system and now I am able to install ncruses 5.9 package (owner iuc). Thank you for helping. Regards, Preeti ...
written 4 months ago by preetipankajakshanpillai0
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Error while installing ncurses 5.9
... I am working with Galaxy local instance. I tried installing ncruses 5.9 package (owner iuc) many times, but every time it is showing error telling **/bin/sh: line 1: patch: command not found**. Due to this, all my tools depending on ncruses 5.9 package is not working. Please, help me to solve this ...

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