Question

Where do I get a WES dataset of size <1GB

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2.7 years ago

pragnapcu • 0

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

WGS WES genomics • 1.3k views

ADD COMMENT • link updated 2.7 years ago by German.M.Demidov ★ 2.9k • written 2.7 years ago by pragnapcu • 0

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what do you mean WES dataset?

ADD REPLY • link 2.7 years ago by German.M.Demidov ★ 2.9k

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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.

ADD REPLY • link 2.7 years ago by pragnapcu • 0

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

ADD REPLY • link 2.7 years ago by GenoMax 141k

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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

ADD REPLY • link 2.7 years ago by German.M.Demidov ★ 2.9k

score 2 · Answer 1 · 2021-08-10

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.