I have short reads from SOLID5500XL sequencing platform. The reads are in '.xsq' format. I have used XSQ tools from life technologies http://www.lifetechnologies.com/fi/en/home/technical-resources/software-downloads/xsq-software.html to convert .xsq to .csfasta and .qual files as shown below;
xsqconvert -c FRAG_BC_01_Can19.xsq
which results in
FRAG_BC_01_Can19_F3.csfasta and FRAG_BC_01_Can19_F3.qual files.
Then i have used 'qualfa2fq.pl' script from bwa to convert to fastq format as shown below:
qualfa2fq.pl FRAG_BC_06_Can19_F3.csfasta FRAG_BC_06_Can19_F3.QV.qual
The fastq file still has the base pairs in color space format. My goal is to detect SNP's by aligning to reference genome. For this purpose i would need the data in base space format. Could someone help to do this?
Any help is highly valuable.