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Old 04-04-2016, 10:04 AM   #3
mikeusyk
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Location: NYC

Join Date: Apr 2016
Posts: 4
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Thank you for your response Ryan. There I quality trim the reads beforehand with print-seq. I did think that it could be the misalignment in the tails that is causing the issue and actually tries over trimming by 20+ bases. This did not help. I made the alignment with vanilla bwa and used the bisulfite converted reference from bismark.

Thank you for pointing me towards bwa-meth. It looks promising and I will likely just switch to it if I cannot get the bowtie to work properly.
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