User: arash.iranzadeh1980

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Posts by arash.iranzadeh1980

<prev • 10 results • page 1 of 1 • next >
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Any GWAS tool for bacteria?
... Hi, I have a vcf file containing 210000 variants (SNPs and INDELS) and 1480 individuals from streptococcus pneumonia bacterium. I need a tool to perform a GWAS on this set of variants. Any tool suggestion? ...
any gwas tool for bacteria? written 23 days ago by arash.iranzadeh198010 • updated 23 days ago by natasha.sernova2.7k
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SNP statistical analysis
... Hi, I am doing a genome wide association study on a series of SNPs. I have confronted many statistical tests like logistic regression, fisher exact test, association test, Chi square etc. Is there any good reference or reading materials for studying these tests on SNPs. I need examples with numerica ...
snp statistical analysis written 27 days ago by arash.iranzadeh198010 • updated 26 days ago by AlexRT10
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Comment: C: VCF file analysis to find genome wide association
... Thank you very much, seems useful. ...
written 12 weeks ago by arash.iranzadeh198010
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VCF file analysis to find genome wide association
... Hi, I have a huge vcf file (2.6 GB) including 1500 individuals from three phenotypes (500 individual from each phenotype). It contains 203846 SNPs and 7174 INDELs. The organism is pneumococcus which is a haploid bacterium. I want to perform a genome wide association study in order to find significa ...
vcf file analysis to find genome wide association written 12 weeks ago by arash.iranzadeh198010 • updated 12 weeks ago by Kevin Blighe9.3k
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Biological Databases Geographical Distribution
... Hi, I am interested to know how biological databases have been distributed worldwide? I think most of them are located in US and Europe. Am I right? Any other important country involved? ...
biological databses geographical distribution written 3 months ago by arash.iranzadeh198010 • updated 3 months ago by Pierre Lindenbaum102k
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Joint variant calling
... Hi, I have 1500 bacterial clean and sorted alignment bam file and I want to call variant and produce a multisample vcf file including 1500 samples. I am going to use GATK and bcftools and then compare results. Bacteria are haploid. In the following commands, -ploidy must be set to 1 or 1500? bcfto ...
joint variant calling written 3 months ago by arash.iranzadeh198010
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Short read alignment to pangenome
... Hi, I have a pangenome graph in dot format. I want to align short reads (fastq) to this graph. I tested vg but I got error (core dumped), any other tool for mapping reads to graph? ...
short read alignment to a pangenome graph written 4 months ago by arash.iranzadeh198010 • updated 3 months ago by Biostar ♦♦ 20
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Converting dot to json
... Hi, I have a pan-genome graph file in dot format, anybody knows how to convert graph file in dot format into json format? ...
genome written 5 months ago by arash.iranzadeh198010 • updated 5 months ago by Alex Reynolds22k
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Variant calling and downstream analysis
... Hi, I have whole genome sequencing data of 1605 bacterial samples in paired-end reads fastq format. These samples come from 3 phenotypes. I have also a reference sequence fasta file. I have aligned 1600 samples to the reference genome and then I passed bam files to samtools mpileup: samtools mpil ...
next-gen snp written 5 months ago by arash.iranzadeh198010 • updated 5 months ago by Brian Bushnell15k
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Any tools to detect lncRNAs from RNA-seq data?
... Hi, I have a set of RNA-seq data, extracted from different conditions plus the genome, the transcriptome and the genome annotation. I would like to detect lncRNA from RNA-seq data. Any tool available for this? ...
rna-seq written 10 months ago by arash.iranzadeh198010 • updated 10 months ago by EagleEye4.8k

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