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.
1 answer
It's true, that ArrayExpress requires trimming. I have to do it before submission, it was in 2019, but I think nothing changes till then. In fact I find it strange, I'd also expect raw files as adapter trimming could be done in different ways. I think you can ask authors of the submission for really raw files.
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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.