Paired End adapter trimming

Question

[bioinformaticsfilesdrive]

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

[st.ph.n]

Do I need to use PEAR at all?

What are you trying to do?

Do I need to use PEAR to combine them before adapter removal and cleaning?

Remove adapters and QC before anything else.

[bioinformaticsfilesdrive]

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

Answer 1

[h.mon]

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.