Question: How to choose values in trimmomatic steps ?
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gravatar for aman.deep13023
5 months ago by
aman.deep130230 wrote:

which one file to choose the adapter sequences to use and what are the value to choose for Maximum mismatch count which will still allow a full match to be performed ? How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment ? How accurate the match between any adapter etc. sequence must be against a read? and in trimmomatic opretion .

galaxy • 212 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson24k • written 5 months ago by aman.deep130230
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gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

How to perform QA on your data depends on the fastq content and the downstream analysis to be performed.

Many of the Galaxy tutorials cover QA steps and can be found here: https://galaxyproject.org/learn/

Trimmomatic is one choice for trimming. The tool itself (the algorithms) and parameters (the usage) are described here and most options are implemented in the Galaxy wrapped version of the tool: http://www.usadellab.org/cms/index.php?page=trimmomatic

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson24k

Thanks Mam, it is working

ADD REPLYlink written 5 months ago by aman.deep130230
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