Raw data clean up
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2.6 years ago
tsomakiank ▴ 50

Hello to everyone. I am new to bioinformatics and I have a beginners question. What can I do with low quality reads. The only thing that I found out so far is that I can trim off the low quality part of the read. Is it something else that I can do to clean up the data? Is there any rule of how much I can trim a read? Thanks in advance!

cleanup rawdata • 688 views
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2.6 years ago

Don't worry too much about low-quality reads.

Worry more about what to do with good quality reads :-)

Few if any analyses are severely impacted merely because the data recovery could have been done better. Even the simplest tasks you undertake will fix 90% of problems, so the best to move onto the main tasks.

In a nutshell run fastp and it will take care of most problems for you

https://github.com/OpenGene/fastp

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Got it! Thanks a lot for your help Istvan

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