Hi there, I currently have SOLiD colorspace data that is paired end (x_F3.fastq and x_F5.fastq). Do I need to use PEAR to combine them before adapter removal and cleaning? Do I need to use PEAR at all?
Thanks for any and all help!
Sincerely,
bioinformaticsfilesdrive
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bioinformaticsfilesdrive •
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The end goal (what I am trying to do) is to map these reads to the mouse reference genome for differential gene expression
Based on your comment, I think the best approach is to map the reads in colorspace using local alignment, which will soft-clip mismatch regions, so adapters wouldn't pose much of a problem.
I would not combine reads with PEAR, you will have a mix of single and paired reads and that would introduce unnecessary complications on the differential gene expression analysis.
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What are you trying to do?
Remove adapters and QC before anything else.
I will remove adapters and QC before thanks!
The end goal (what I am trying to do) is to map these reads to the mouse reference genome for differential gene expression