Trimmomatic

Question

[wonde2000]

Dear All, when I trim adapters and remove sequences below 20 phred scales, the sequence length was sowed to the right. Therefore, is it possible to continue with the trimmed sequence or this may cause a problem in the downstream analysis? Thank you in advance for your valuable suggestions.

Answer 1

[Meisam]

Yes it is totally expected, since most of the low quality bases are toward the reads end, the tails are getting chewed until the rest of the read is high score and kept, so not all reads gonna be the same length anymore. It is generally good practice to also set the "MINLEN" option so if a trimmed read gets shorter than a threshold it is no longer kept.