Raw data clean up

Question

[tsomakiank]

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!

Answer 1

[Istvan Albert]

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

[tsomakiank]

Got it! Thanks a lot for your help Istvan