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Old 04-17-2017, 01:17 PM   #132
pig_raffles
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Location: Sheffield, UK

Join Date: Feb 2012
Posts: 18
Default Choosing minimum RRBS read length in Trim Galore!

I am new to the bioinformatic analysis of RRBS data. I am using Trim Galore! to QC and adapter trim my RRBS read data. I have generated single-end 75bp reads on an Illumina NextSeq.

The default minimum read length parameter in Trim Galore! is 20 bp but I was wondering if there were any practical considerations for alignment/mapping of reads to take into account when choosing a minimum read length and if anyone had any tips on optimizing this parameter?
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