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Old 07-08-2018, 11:28 AM   #121
kokyriakidis
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Default RQCFilter Norm and EC

Hi Brian,

I am trying to trim and filter my data with RQCFilter but I cannot find an option for normalisation and error correction. Are there any parameters in this package? Also there is a parameter called -merge. Does it do merging? Should I set it to false and try normalising and error correcting first?
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Old 07-08-2018, 12:37 PM   #122
GenoMax
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Can you clarify which program you are referring to? I don't think there is a RQCfilter program in BBMap suite.
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Old 07-08-2018, 01:11 PM   #123
kokyriakidis
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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 01:15 PM.
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Old 07-08-2018, 11:19 PM   #124
GenoMax
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Since notes on the page you linked say this:
Quote:
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.
You should follow the steps that are denoted to replicate that functionality on the linked page.

In general @Brian has recommended merging reads before doing any additional manipulations.
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Old 07-08-2018, 11:25 PM   #125
kokyriakidis
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Quote:
Originally Posted by GenoMax View Post
Since notes on the page you linked say this:


You should follow the steps that are denoted to replicate that functionality on the linked page.

In general @Brian has recommended merging reads before doing any additional manipulations.
In long pair mate reads I just do the splitNextera extra step? Otherwise the pipeline remains the same?
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Old 07-09-2018, 03:26 AM   #126
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I would think so. I don't have first hand experience with mate pair reads but I recall that you need to switch one of the reads around.
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Old 08-06-2018, 04:16 PM   #127
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BBMerge guide recommends trimming adapters before merging -- but also, in a different place, recommends providing the adapter sequences to BBMerge. Which is best?
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