how i can use SRA accession Number to call raw reads ?

Question

[sh_shaddad77]

i have project to align 2 genome . Generated the reference index: bwa index reference.fa Then i want to align the reads to the reference index bwa mem reference.fa reads1.fq reads2.fq > aligned_pairs.sam To download the reads for the second genome , i use the genome deposit SRA accession number to download from ENA . the page present option : FASTQ files (FTP) NCBI SRA file (FTP file1 file1 file2 SRA accession number SRR1779159 which one should be used ?

https://www.ebi.ac.uk/ena/data/view/SRR1779159

Answer 1

[yasokannan93]

Both the options (FASTQ files FTP and NCBI SRA file FTP) can be used. Its the same file.

[ATpoint]

Yep, should be all the same but you would need to convert the sra file to fastq which is additional effort. I always use FASTQ files (FTP), see Fast download of FASTQ files from the European Nucleotide Archive (ENA)