srf2fastq -e option

  • I don't quite understand the meaning of the -e option in srf2illuiman. Can someone please explain what is the type E region? Thank you.

  • James Bonfield
    James Bonfield

    There should be a unix "man page" with srf2fastq which elaborates a bit further:

    Include any explicit sequence (ZTR region chunk of type 'E') in the sequence output. The explicit sequence is also included in the quality line too. Currently this is utilised by ABI SOLiD to store the last base of the primer.

    Basically, each sequence in an SRF rile has a region chunk which outlines where the first and second read start and end in a read-pair, perhaps with a third region indicating an indexed sample too. In all of these cases the region indicates the location and size of a piece of DNA listed in the trace file itself.  There is also the option of creating "explicit" regions which are bases we may want output along too, but those bases do not actually exist in the trace itself.

    The current example usage of this is for ABI SOLiD runs where we typically have a primer base followed by a bunch of colours, eg T0122301010322. The "T" is the explicit base and will be output if we use srf2fastq -e.