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Old 11-22-2015, 07:02 PM   #1
bluepoison
Junior Member
 
Location: Detroit

Join Date: Nov 2015
Posts: 4
Default finding adapters for trimming

Hi All,

I am a total newbies in this field. I want to know the trend of the community for adapter trimming steps.

I have got 50bp single end reads (Sanger / Illumina 1.9). Primary goal is to align the reads using bismark, and then extract methylation scores using 'methylkit'. There were three overrepresented sequences in FastQC report. Then I ran trim_galore using the default settings. trim_galore(which basically uses 'cutadapt') trimmed the universal adapter but still there are two overrepresented sequences left in the fastQC report.

I have read so many posts related to trimming last 3-4 days but still I am so confused. The summary I have got is that FastQC tells us about adapter contamination, but it may not tell about the actual adapter sequence.

1. Is it a MUST to trim all the overrepresented sequences or just trimming the universal adapter is fine?
2. What is the easiest way to find the sequences that need to be trimmed?

Any help/suggestion is greatly appreciated.
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