User: zhou_1228

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zhou_12280
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Posts by zhou_1228

<prev • 11 results • page 1 of 2 • next >
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Display SNPs in VCF files generated by CRISP
... I generated large amount of vcf files through CRISP to identify SNPs in every sample. Each vcf files represents a gene. I can check SNPs in some vcf files using IGV software while there is no SNPs displayed in other vcf files. However, I can see a series of SNPs from latter vcf files if I open them ...
snp written 9 days ago by zhou_12280
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Comment: C: Using freebayes to call variants
... 24 or 48 means there are 24 genomic DNAs in one well, and 48 genomic DNAs in another well. ...
written 7 months ago by zhou_12280
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Using freebayes to call variants
... I am using freebayes package to call SNPs from reads generated from NGS. It works well when I ran samples with 24 genome copies, however, the program got killed when I process samples with 48 genome copies using a local PC or it took about 10 hours to finish one sample when I ran it on a cluster. I ...
next-gen freebayes sequencing written 7 months ago by zhou_12280 • updated 7 months ago by finswimmer11k
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Comment: C: Automating to convert multiple fastq files into one fastq file
... I got it. Thank you so much. ...
written 7 months ago by zhou_12280
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Comment: C: Automating to convert multiple fastq files into one fastq file
... Thank you so much for your reply. I found that there are many GNU parallel package for downloading. My OS is Linux Mint 18.1, so which one I should download? Thank you. ...
written 7 months ago by zhou_12280
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Comment: C: Automating to convert multiple fastq files into one fastq file
... From my understanding, you run two commands, cat and bwa together in your model. But in my case, for each sample, I firstly need merge three *R1*.fastq files into one *-F*.fastq and another three *R2*.fastq to one *-R*.fastq, separately. And then run command "bwa mem GMbwaidx *-F*.fastq *-R*.fastq & ...
written 8 months ago by zhou_12280
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Comment: C: Automating to convert multiple fastq files into one fastq file
... P001_WB01 represent plate 1, well No. B1 ...
written 8 months ago by zhou_12280
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Automating to convert multiple fastq files into one fastq file
... I got six fastq files (three forward and three reverse) for every sample in 96-well plate via NGS. As the first step of SNP calling, I need convert these six files into two files (forward and reverse fastq file) for each sample. Now I am trying to write a shell scripts to automatically merge every t ...
snp sequencing written 8 months ago by zhou_12280 • updated 8 months ago by Malcolm.Cook1.0k
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Automating a SNP calling workflow
... I wrote a program to automate SNP calling process, but not sure if it works since I am new to shell scricpts. If I can get some review for the scripts, I would highly appreciate your help. The below is scripts, cd ~/results genome=~/home/administrator/GlycinMaxNew.fasta mkdir ...
next-gen snp sequencing written 8 months ago by zhou_12280 • updated 8 months ago by msimmer92200
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Comment: C: Difference in output VCF between running on a local PC and supercomputer cluster
... Hi Pierre, thanks for your reply. Yes, I checked the versions of all three tools, BWA, samtools, and freebayes in my SNP calling program, and they are the same between local PC and supercomputer cluster. However, I noticed that the size of final VCF file are different, 19.9MB on supercomputer and 23 ...
written 8 months ago by zhou_12280

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