I just started using the SRA toolkit but I am quite puzzled about what I have. I downloaded an SRA file with fasterq-dump. The data is indicated to be paired-end and I do get two fastq files. However, the headers of each read are not in the standard format but rather in SRA format, I suppose.
The first 2 headers of the first fastq file are shown here
@ERX2240357.19 SBS123:200:C3PFWACXX:6:1101:2133:1988 length=101
@ERX2240357.20 SBS123:200:C3PFWACXX:6:1101:2347:1955 length=101
And the first 2 headers of the second fastq file are shown here
@ERX2240357.1 SBS123:200:C3PFWACXX:6:1101:1462:1956 length=101
@ERX2240357.2 SBS123:200:C3PFWACXX:6:1101:1487:1970 length=101
Normally I can see the pairs by looking at /1 and /2 in the header, but now this is missing. How can tools like bwa mem recognize that two reads form a pair based on the headers in the above SRA format?
I looked up the documentation but it doesn't get more clear for me...