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Old 07-08-2018, 12:11 PM   #123
kokyriakidis
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Location: Thessaloniki, Greece

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Source: https://jgi.doe.gov/data-and-tools/b...preprocessing/

"These steps replicate the QA protocol implemented at JGI for Illumina reads. There is a program “RQCFilter” which implements them as a pipeline, but that is not publically available because it has numerous hard-coded paths to reference datasets of contaminants."

It is in the bbtools files.

Nevermind! 1) Is it a good plan to normalise and error correct first BEFORE merging? 2) Do I need to follow a different approach at trimming and filtering short vs long mate pair reads (Nextera)?

Last edited by kokyriakidis; 07-08-2018 at 12:15 PM.
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