srf_info(1) [debian man page]
srf_info(1) Staden io_lib srf_info(1) NAME
srf_info - Lists information about the contents of an SRF file SYNOPSIS
srf_info [-l bitmap] srf_archive ... DESCRIPTION
srf_info lists some simple frequency metrics on the contents of an SRF file, both in terms of how many traces there are and the sort of data held within them. For efficiencies sake some control is given over which statistics to gather and display. This is controlled by the -l level parameter. The value is the summation of one or more of the following values, representing the data to display. 1 Count of good/bad reads. 2 Counts and compressed size for selected chunk types. 4 Trace count and trace name prefix for each trace_header. 8 Base count. OPTIONS
-l bitmap Controls which statistics to gather and display. Bitmap is a value from 0 to 15 (1+2+4+8) as described in the DESCRIPTION section above. EXAMPLES
To count the total number of good and bad reads along with a break down of trace names per SRF data-block-header we would use bitmap values 1 and 4 combined. srf_info -l 5 foo.srf To count the total number of reads for all srf files in a directory. srf_info -l 1 *.srf AUTHOR
Steven Leonard, Wellcome Trust Sanger Institute September 19 srf_info(1)
Check Out this Related Man Page
srf2fastq(1) Staden io_lib srf2fastq(1) NAME
srf2fastq - Converts SRF files to Sanger fastq format SYNOPSIS
srf2fastq [options] srf_archive ... DESCRIPTION
srf2fastq extracts sequences and qualities from one or more SRF archives and writes them in Sanger fastq format to stdout. Note that Illumina also have a fastq format (used in the GERALD directories) which differs slightly in the use of log-odds scores for the quality values. The format described here is using the traditional Phred style of quality encoding. OPTIONS
-c Outputs calibrated confidence values using the ZTR CNF1 chunk type for a single quality per base. Without this use the original Illumina _prb.txt files consisting of four quality values per base, stored in the ZTR CNF4 chunks. -C Masks out sequences tagged as bad quality. -s root Generates files on disk with filenames starting root, one file per non-explicit element in the SRF/ZTR region (REGN) chunk. Typi- cally this results in two files for paired end runs. The filename suffixes come from the names listed in the SRF region chunks. This option conflicts with the -S parameter. -S Splits sequences into regions, but sequentially lists each sequence region to stdout instead of splitting to separate files on disk. This option conflicts with the -s parameter. -n When using -s the filename suffixes are simply numbered (starting with 1) instead of using the names listed in the SRF region chunks. -a Appends region index to the sequence names. Ie generate "name/1" and "name/2" for a paired read. -e 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. -r region list Reverse complements the sequence and reverses the quality values for all regions in the region list. This is a comma separated list of integer values enumerating the regions, starting from 1. Note that this option only works when either -s or -S are specified. EXAMPLES
To extract only the good quality sequences from all srf files in the current directory using calibrated confidence values (if available). srf2fastq -c -C *.srf > runX.fastq To extract a paired end run into two separate files with sequences named name/1 and name/2. srf2fastq -s runX -a -n runX.srf To extract a paired end run as a single file, alternating forward and reverse sequences, with the second read being reverse complemented. srf2fastq -S -r 2 runX.srf > runX.fastq AUTHOR
James Bonfield, Steven Leonard - Wellcome Trust Sanger Institute December 10 srf2fastq(1)