Hi, I am using RNA-Seq data from ArrayExpress and I'm having difficulty finding out whether its necessary to use some software to remove adapter sequences. The FASTQ submission specifications state that no technical adapter sequences are allowed which suggest that the adapter sequences should already be removed but it could also be stating not to submit an adapter sequence FASTQ file. I'm having difficulty finding information on this so any insight is appreciated.
Scanning/trimming data files takes a bit of time but will ensure that there is no extraneous sequence left when you use the data for other analysis. One quick check would be to see if all the reads are of same length as the length of sequencing. If true this could be an indication that the data has not been trimmed.