adaptors removal before using bowtie for bam generation (from fastq)

Question

[S]

Hello,

I would like to run AS analysis using rMATS from 2 reps of human rna-seq data (2 fastq files - single end), I first ran fastqc on the files and got that there are illumina universal adaptors - should I remove them using for example cutadapt before using bowtie2 for the bam generation ? where can I find the adaptor sequence?

Thanks :)

Answer 1

[ATpoint]

See What is the right illumina universal adapter sequence for trimming paired-end reads?

Note that for typical RNA-seq alignment you should use a spice-aware aligner, such as STAR, unless the combination of bowtie2 and rMATS is well-established (idk).