Paired End adapter trimming
1
0
Entering edit mode
4.3 years ago

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

RNA-Seq next-gen sequencing SOLiD • 1.0k views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.3 years ago
h.mon 33k

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.

ADD COMMENT

Login before adding your answer.

Traffic: 2763 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6