how to removed the nucleotides from a fastq file (single-end) in conditional

Question

[17318598206]

"For reads beginning with GGG including (NGG, NNG or GNG) and ending with three or more adenosines, we removed the first three nucleotides and mapped the remaining sequence with and without the tailing adenosines to the mouse genome using TopHat 2.0.4." so, what should i code

[Dunois]

Take a look at cutadapt or Trimmomatic.