Methodology used by Fastx clipper

[babi2305]

Hello everyone,

Can somebody tell me here the methodology used by Fastx clipper to trim reads? and if possible about cutadapt also..?? I am using FastX clipper to trim single end adapters (at 3') for illumina RNA seq data with indexes (although indexes has been already removed from fastq files). Reads are 50 bases long. Is that a good choice?


Thanks, and by the way this is an awesome forum.