download fastq based on fasta file of bacteria genomes

Question

[ali_karimnezhad]

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.

Answer 1

[lieven.sterck]

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 )

[ali_karimnezhad]

Many thanks lieven.sterck, GenoMax .

Answer 2

[GenoMax]

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