Ab Solid Fastq To Illumina Fastq

Question

[Varun Gupta]

HI Everyone

I have AB solid data The fastq file looks like this

@SRR334700.1 solid0527_20110502_FRAG_BC_ReidWT_bcSample1_ReidWT_1_5_16 length=50
T120202210232000020002.00301000012.100...00........
+SRR334700.1 solid0527_20110502_FRAG_BC_ReidWT_bcSample1_ReidWT_1_5_16 length=50
!/<%2/:%*)-%%0'--'')/.!%('1'%),+/%!&',!!!'+!!!!!!!!

I have dealt with only illumina fastq files. Can you tell me how can i convert it into a format of illumina fastq files. Moreover what would be the difference between illumina fastq and solexa fastq and sanger fastq format

Regards

Varun

[brentp]

you can read up on colorspace here: Is Conversion From Colorspace To Base Space Lossy? or with this tag: http://biostars.org/show/tag/colorspace/

you don't want to convert the format to Illumina. Do the mapping in colorspace and use that alignment.

Answer 1

[JC]

As @brentp pointed, you don't need to convert to base space, you can use the color space with Bowtie/TopHat, Novoalign, SHiRMP and other mappers and even assemblers. The major difference between the FASTQ formats are in the quality scores scale used, wikipedia has a good table for that: http://en.wikipedia.org/wiki/Fastq