download sequencing data from public domain

Question

[Sara]

I am trying to get sequencing data from a paper (with accession number) from “https://www.ebi.ac.uk/ena/” OR from “https://trace.ncbi.nlm.nih.gov/Traces/sra/”and I am sure there should be R1 and R2 per sample but I only find one file per sample. Do you know what could be the reason for that?

Answer 1

[Mensur Dlakic]

Do you know what could be the reason for that?

Samples could be with unpaired reads, or with interleaved paired reads. It is impossible to tell without knowing the sample accession number. If the latter is the case, you can split the reads into R1 and R2 using reformat.sh from the BBTools package.

Answer 2

[patrickdm]

Just a guess, for downloads from NCBI SRA proabably you'd have to use the fastq-dump tool to convert the SRA data into R1+R2 in fastq format. Hth