Recently I got my sequencing data based on SOLiD system. For each sample I got two .csfasta files labled 1 and 2, and two .qual files corresponding to the csfasta file. Since I am quite new to this high throughput sequencing technology, I don't know how to use the .qual file for analysis. I know the .csfasta files contain the sequence data which are in color space format. I am able to convert the color space sequences to base space. So can i just use the csfasta file for the following analysis, such as trimming adaptor, alignment, and statistical analysis, without the .qual file?
And the two .csfasta files (1 and 2) can be pooled together for analysis?
Hope to get your help. Thank you in advance.
And the two .csfasta files (1 and 2) can be pooled together for analysis?
Hope to get your help. Thank you in advance.
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