User: rizky_dsatrio

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Posts by rizky_dsatrio

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Inreasing memory usage in bcftools
... @Pierre Lindenbaum Thank you for the command-line advice, now I can see what's happening during the process. ...
written 3 months ago by rizky_dsatrio0
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Comment: C: Inreasing memory usage in bcftools
... Thanks for your comment @WouterDeCoster Can we accelerate the process by increasing the RAM usage? ...
written 3 months ago by rizky_dsatrio0
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Inreasing memory usage in bcftools
... Hello I am a beginner in ngs bioinformatic analysis. I try to create a multisampled .vcf file from 250 .bam file using mpileup bcftools. Here the command I use: bcftools mpileup -O z -o output.vcf.gz -f ref_genome.fasta bam_file_list*.bam There are two questions I want to ask about this. 1. ...
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Comment: C: DNA Integrity in Whole Genome Sequencing
... Dear h.mon Thank you for your comment. How do you think about the downstream analysis that may be affected by low integrity DNA? If sonication step produces fragmented (small-size) DNA, why low integrity DNA can affect the sequencing quality or downstream analysis? Regards ...
written 8 months ago by rizky_dsatrio0
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DNA Integrity in Whole Genome Sequencing
... How important DNA integrity in the whole genome resequencing? If the early step of the library construction is DNA fragmentation (sonication), why NGS companies reject the sample that has degradation, or fragment size lower than 20kb? ...
genome next-gen sequencing written 8 months ago by rizky_dsatrio0
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Which SNP is the best to use for GWAS from SNP-seek (IRRI) data set?
... I want to do GWAS in rice. There are several SNP data set from 3000 rice accessions provided by IRRI (http://snp-seek.irri.org) i.e: 1. all (32M) 2. base (18M) 3. filtered (4.8M) 4. core (404k) However, I only use 300 accessions from those. Which data set I should use for genotyping in my GWAS anal ...
gwas snp-seek snp genotyping written 8 months ago by rizky_dsatrio0
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Differences in the number of genotyping data for GWAS
... If we want to do GWAS in agriculture, which is the better option among these cases: 1. I get 200 whole-genome data and also 200 plant accessions. I use 200 whole-genome data for SNP-calling and GWAS analysis. 2. I get 2000 whole-genome data, but I only have 200 plant accessions. I use 2000 whole-g ...
gwas snp written 9 months ago by rizky_dsatrio0

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