download fastq based on fasta file of bacteria genomes
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5 months ago

I am trying to replicate the SNP calling analysis done in this paper,

Genomic Variation and Evolution of Vibrio parahaemolyticus ST36 over the Course of a Transcontinental Epidemic Expansion.

It uses a reference genome with BioSample id SAMN03255431 and a couple of other genomes with Biosamples ids (SAMN03945137,SAMN03945136,...). My understanding is that for SNP calling fastq files are needed but with the BioSample id SAMN03255431 I only see a fatsta file on ncbi. I wonder how I could retrieve the corresponding fastq files to replicate the SNP calling.

bacteria SNPcalling fastq fasta • 306 views
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5 months ago

from those SAMN numbers you can get to the BioProject number (eg. PRJNA245882 ) . Under those numbers you can get to the SRA experiments (== hold the actual read data).

that being said: it seems to be from quite a big project (multi-sample/mutli-species) so you might need to look for the correct SRA files.

UPDATE: or go to ENA as GenoMax points out (generally much easier to get the data you are looking for from them than NCBI-SRA )

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Many thanks lieven.sterck, GenoMax .

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5 months ago
GenoMax 108k

You can find the fastq files for the samples at EBI-ENA. example of SAMN03255431

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