Many thanks lieven.sterck, GenoMax .
• 0 views
•
link
written
by
ali_karimnezhad •
download fastq based on fasta file of bacteria genomes
I am trying to replicate the SNP calling analysis done in this paper,
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.
• 1,987 views
•
link
written
by
ali_karimnezhad •
2 answers
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 )
• 0 views
•
link
written
by
lieven.sterck
You can find the fastq files for the samples at EBI-ENA. example of SAMN03255431
Log in to answer this question.