Dr. Nekrutenko, I've found the fq_all2std.pl script distributed with Maq to be very helpful for converting file formats to a standardized Fastq. Because it's so small (10K) I'll attach it to this email for anyone interested. Also, I'll copy its usage notes here so you can see the formats it converts: Usage: fq_all2std.pl <command> <in.txt> Command: scarf2std Convert SCARF format to the standard/Sanger FASTQ fqint2std Convert FASTQ-int format to the standard/Sanger F ASTQ sol2std Convert Solexa/Illumina FASTQ to the standard FAS TQ std2sol Convert standard FASTQ to Solexa/Illumina FASTQ ( simplified) fa2std Convert FASTA to the standard FASTQ seqprb2std Convert .seq and .prb files to the standard FASTQ fq2fa Convert various FASTQ-like format to FASTA export2sol Convert Solexa export format to Solexa FASTQ export2std Convert Solexa export format to Sanger FASTQ csfa2std Convert AB SOLiD read format to Sanger FASTQ std2qual Convert standard FASTQ to .seq+.qual instruction Explanation to different format example Show examples of various formats Note: Read/quality sequences MUST be presented in one line. John Obenauer On Tuesday 21 July 2009 03:39:16 pm Anton Nekrutenko wrote:
Hiram:
Can you share the code? Which baseQ scaling are you using (Sanger| Solexa)? SOliD support?
Thanks,
anton
On Jul 21, 2009, at 4:35 PM, Hiram Clawson wrote:
I've written a fastq parser here.
Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org
_______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
-- John Obenauer, Ph.D. Bioinformatics Group Leader Information Sciences Department St. Jude Children's Research Hospital 262 Danny Thomas Place Mail Stop 312 Memphis, TN 38105 (901) 595-3188 john.obenauer@stjude.org Email Disclaimer: www.stjude.org/emaildisclaimer