After Trim galore!, fastqc show the seuqence length is 20-151

Question

[Jiahui]

Hi all, I run fastqc and multiqc and found that my RNA-seq has adaptors exists, after using trim galore! I run fastqc to see if the QC could be better, but the results show that the sequence length becomes a range that is from 20-151. I need a specific sequence length to do RNA-star. But now it turned out to be a range, can anyone help me? btw, I tried cutadapt, but after cutadapt, I run fastqc, and it shows the adaptor is still there.

Answer 1

[GenoMax]

It is normal and expected. Once a trimming program removes part of the read you are going to end up with a range of lengths.

By the way, you don't strictly need to pre-trim the data since an aligner can handle non-aligning parts of a read by "soft-clipping" them.

[Jiahui]

so you mean i dont have to trim the rna-seq, just run mapping? but I cannot remove the adaptors, would that be a problem for mapping?

[GenoMax]

Modern aligners will remove parts of a read that do not map (which will include adapter sequence) by doing "clipping". If you intend to do any de novo assembly then you do need to remove adapter/extraneous sequence by trimming.

[Jiahui]

thank you! do you have any recommendations on aligners that I can use?

[GenoMax]

If you need a splice aware aligner then STAR, bbmap, HISAT2 are good choices. If you have prokaryotic data then most NGS aligners should work since you do not need to account for splicing.