trimm data before analysis

Question

[askari.arezou94]

hello every one i have 25 raw data ,after quality control ,the quality of sequences was very high and don't have any adaptor, lenght of reads are 50 bp. it is necessary using from trimmomatic before start to analysis data?

[askari.arezou94]

thank you so much for your response.

Answer 1

[GenoMax]

If you are aligning to a good reference they you can omit trimming. Most aligners should be able to deal with bases that do not align (e.g. soft-clip them). If you are going to do any de novo assembly you should scan/trim your data.

[askari.arezou94]

in fastqc results all of the outputs should be confirmed? if per base sequence content and GC Content ,sequence duplicate level and overrepresent content is not confirmed, what should i do?

[GenoMax]

Since you tagged this rnaseq please read these blog posts by authors of FastQC that address your questions.
https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/
https://sequencing.qcfail.com/articles/libraries-can-contain-technical-duplication/

FastQC is a QC program. It uses parameter intervals for genomic sequencing to make its judgement calls (these can be changed). Having a test FAIL does not automatically mean that the data is bad. You have to take always FastQC results in context of the type of data being analyzed.

[askari.arezou94]

thank you. my data is transcriptomic data

Answer 2

[yoh1242]

If your sequences are of high quality and no adapter sequences are attached then YES you can skip trimming and move towards the next step.