The SRF file format is a binary format for "Sequence Read Format". Some documentation can be found at the srf project page. The ools are from the staden io lib sub package.

If you get the error message Zero or greater than one CNF chunks found with srf2fastq, you can use srf2fastq -c to tell it to use the older 4 value confidence value format.

Examples

srf2fastq woldlab_081224_HWI-EAS229_0082_30HGGAAXX_4.srf > 30HGGAAXX_4.fastq

or

srf2fastq -c woldlab_081224_HWI-EAS229_0082_30HGGAAXX_4.srf > 30HGGAAXX_4.fastq

To split a paired-end srf file into two fastq files:

srf2fastq -s 10689-FI_AU_8_M_MB4721_S1-3120JAAXX_l6_r -a -n -c woldlab_090417_HWI-EAS229_0109_3120JAAXX_6.srf

Notes

I don't know of a good way to tell which format a srf file is without just checking to see if the command fails.

srf (last edited 2011-10-13 19:06:28 by hamrhein)