Hi all, I've got some "Sanger" capillary sequence files in ABI trace file format, which I understand includes the probabilities of the 4 bases along the sequencing run. I'd like to extract this as a FASTQ file with meaningful quality scores based on the trace data (for use in assembly).
This doesn't seem to work - the FASTQ quality score characters are all double quotes (ASCI 34), meaning PHRED quality 1. seqret -sformat abi -osformat fastq-sanger -sequence example.ab1 -outseq example.fastq -auto Output as FASTA seems fine: seqret -sformat abi -osformat fasta -sequence example.ab1 -outseq example.fasta -auto Is ABI to FASTQ a reasonable to expect seqret to support? If so, could it be added to the TODO list please? Peter C. P.S. I'd be interested to hear suggestions for alternative tools to tackle this conversion. _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
