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Old 04-18-2017, 01:04 AM   #133
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Originally Posted by pig_raffles View Post
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?
Very short reads generally don't tend to align uniquely in bisulfite-seq mapping because the three letter alignment allows more ambiguous alignments. In that sense the shortness of reads sorts itself out in a way. Some programs however don't like it (or didn't like it in the past) when the sequence entry is extremely short or even empty, which is why we are introducing a short (but arbitrary) cutoff. I hope this helps.
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