[EMBOSS] ABI to FASTQ with seqret

[Peter Rice]

On 22/07/10 12:22, Peter C. wrote:

>> I truncated this for brevity. Here the quality string repeats ASCI 34, ASCI 33
>> (PHRED quality 1, quality 0) which is rather strange. The sequence appears
>> to agree with the provided file pGEM_(ABI)_A01.seq
>>
>> Have I just been unlucky with the AB1 files that I have looked at? Thus
>> far all the quality scores seem meaningless.

There are two sets of quality scores in that file. Both are the
alternating characters 1 and 0. Adding 33 gives the scores you see.

Looks as though EMBOSS is just reporting what it finds.

The file offset is the value returned by function
ajSeqABIGetConfidOffset. It simply reads one byte from there for each
base of sequence length.


> I went back through my old emails, and see you had been testing with
> http://www.appliedbiosystems.com/support/software_community/ab1_files.zip
> (I had trouble downloading this with curl - Firefox worked). Looking at these
> ABI files with seqret as FASTQ does seem to give meaningful quality scores.
> Curious.

It should look for a PCON tag in the file and pick up the second of two,
or the first if there is only one.

Can anyone on the list enlighten us further on what is intended for the
quality socrss in these example files?

regards,

Peter Rice