About Data Format and Eland Input

[foolishbrat]

Hi all,

I have couple of questions regarding above topic:

1. What is the name of data format below?
2. And can Eland take it as input?
3. How can I convert it into FASTA?

4       1       998     538     GAAG...T..AA....C..T...A............
4       1       955     536     GGGTTTGTAACTTTATTCTTTATATTAAGACTCATT
4       1       117     123     GTTCTGGTGTCTAACTTTATTCTACCCCTAGAACAC
4       1       899     114     GAGTTATTGGAAACAAAATTAAAACACCCATCGCTA
4       1       958     100     GAGTGCACCTATTTATTGCCCACTGCCCTCTTTTTA
4       1       885     618     GGTGCTTTTTAAAACGCTCCAAGTTTTAAAAGTCTT
4       1       876     615     GTTTGATTTGAATAAAATCAAGTATCAATTTACTGA
4       1       880     509     GGTTGTTTGCATGTGATTAAGAATCTTTTATGCATT
4       1       911     582     GATTTCATCCATCACCAACCTCAACCACACAAACAC
4       1       881     107     GTTTTTTTCGCTCAATTCTTTAACCATAAGCGTTTT
4       1       40      113     GATTAAGGGTGTGTTGGGGGTGTTTTAAGGCGTAGG
4       1       934     605     GTTTTTCTAAAGAGGGTTTTATTATTTTTCTCTTTT
4       1       53      78      GCAGAAACGCGCTTTATGTTAAGATCTTCAAAATTG
4       1       13      85      GCCTAGCGATATCGCTAAGGATATTGTGGTAAATCT
4       1       777     754     GCCGTTTTTTTCTATAGTTTTGGGCATTGGTGCTGG

[zee]

This looks like Solexa's SEQ format, there should be a corresponding PRB file with a value for each base, for each position, so if you had a read of 10 bases, there would be 40 values in the PRB format.

Eland can take the PRB format as well as FASTA. If you download the MAQ package and MAQ scripts the fq_all2std.pl should take care of all your format conversion needs e.g.

fq_all2std.pl 

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 FASTQ
         sol2std        Convert Solexa/Illumina FASTQ to the standard FASTQ
         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
         instruction    Explanation to different format
         example        Show examples of various formats

Note:    Read/quality sequences MUST be presented in one line.

[swbarnes2]

Maq's seqprb2std looks like it will work...for one .prb and one seq file. GAI chips have 300 tiles per lane, newer chips 100 per lane. You'd need a wrapper torun the program mutiple times.

Look in a thread called "Illumina's PRB file to FastQ" in 'Bioinformatics" for a Perl script that will turn .seq and .prb files info FASTQ's that'll also need tweaking if you need to keep the lanes separate.

But to turn a raw .seq ito a fasta is pretty easy. A few lines in awk or sed, or a Perl one-liner, maybe.