Where do I get a WES dataset of size <1GB
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10 weeks ago
pragnapcu • 0

Can someone please tell me from where can I get the WES or WGS dataset of size <1GB

WGS WES genomics • 380 views
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what do you mean WES dataset?

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whole-exome sequencing data or whole-genome sequencing data. Please correct me if I am wrong. I have started learning NGS analysis just now. I sincerely appreciate ur suggestions.

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You can always downsample a larger dataset. seqtk, reformat.sh from BBMap are a couple of possible tools.

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yeap but it can be that you need FASTQ files < 1GB, or BAM files < 1GB (which is pretty unrealistic), or VCF files < 1GB. All such files are possibly to be generated from WES

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10 weeks ago
ATpoint 54k

Just browse sra-explorer.info for datasets. I doubt you can meaningfully query for file size as this depends on coverage and read length. Just download any from the species you need and then downsample. Just use head on the fastq files to get like the first 4000000 lines which equals 1mio reads. Reads in fastq files are random and not ordered other than its position on the flow cell, hence you do not strictly need a dedicated sampling approach, especially if this is just for some practicing task.