Not an issue but questions

[FritzPeleke]

Hi I am new to NGS in general and I have a few may be dumb questions.

• When should I use sickle se and when should I use pe?
  -Is it possible to run sickle like in a for loop so it trims like all my fastq files? If yes how
  -could you please elaborate more on its installation or direct me to a tutorial?
  Thanks :)

[pentalpha]

SE is for Single End fastq files and PE for Paired End.
A fastq (or just .fq) file is Paired End when, for each sample sequenced, there's a pair of files instead of just one.
Their names will usually be "something.1.fastq and something.2.fastq" or "something.L.fastq and something.R.fastq".

[FritzPeleke]

Thanks @pentalpha