Short question:
where can I find what F and J and < and - and 7 mean in a Sequence file?

Longer version:
I was looking at this sequence file I got from NCBI (it's an sra file? if that is the correct terminology) and I used the sratoolkit to print out a few spots

looking at them I expected to see ACGU (this was meant to be an RNA sequence), but what I see are like


Where can I find a reference to help me "understand" this?
I mean I assume - means missed or unknown? or is it meant to be already aligned and these are deletions?

I appreciate any pointer to get started. as you must have observed I am a total noob.

I got the file from: https://www.ncbi.nlm.nih.gov/sra/SRX8156420[accn]

Then I did a

 ./fastq-dump -X 5 -Z ERR4557575

Follow-up question:

  • Where do you look for the quality scores ranges and such, I guess as @winnie2k suggested I should convert this to FASTQ and make my life easier, but still wanted to understand the file better.
  • 1
    $\begingroup$ Regarding the follow-up question: SRA files are a red herring. Nobody I know cares about the SRA file format ¯\_(ツ)_/¯ $\endgroup$
    – winni2k
    May 6 at 6:54

I usually convert SRA files to FASTQ before doing any further processing, but the tooling for converting SRA files is cumbersome.

To simplify things, I recommend you download the FASTQ file directly. The ENA currently has a nicer interface for doing these things. Here is a link to download the FASTQ files for the SRA sequencing run associated with the SRA experiment you are describing: https://www.ebi.ac.uk/ena/browser/view/SRR11588968

A description of the FASTQ format can be found here: https://en.wikipedia.org/wiki/FASTQ_format


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