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First script trimmomatic

Hi, I'm a novice user of the trimmomatic program. My task in college is to create a script that will allow me to automate the trimming of 200 samples in turn from a file.

I can do it manually, but I have a problem with creating one script that I will do without my intervention

I am asking for any help. Thank you for all the help

~Daniel

trimmomatic
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updated by Biostar Biostar • written by milord94 • milord94

The idea of an assignment is to do it yourself. What have you tried?

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written by ATpoint ATpoint

Yes, these are my practices and the completion stage will be the creation of this script. The initial attempts were based on the attempt of bash opening the sv file in which the initial trimming script is included. I admit that I am still weak, therefore I do not know exactly where to go and what to learn to do it. Any tips will be useful

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written by milord94 • milord94

Are you familiar with any programming language ? PERL , Python ?

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written by lakhujanivijay lakhujanivijay

At university I learn two programming languages, R studio and Python

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written by milord94 • milord94

Hi milord94,

I would suggest having a read of the book: "Bioinformatics Data Skills" by Vince Buffalo. At chapter 12: "Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing Tasks" you'll find very instructive information, especially in the section: "Processing Files with Bash Using for Loops and Globbing" (page 405).

After you try things, learn things, or break things, you can provide what you've tried, and the error you get. I think people will be glad to help. :-)

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written by AK AK

Thank you, I read the book and talk to you again

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written by milord94 • milord94

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