This is a test version of Biostars. For the public version, visit https://www.biostars.org.
adaptors removal before using bowtie for bam generation (from fastq)

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 :)

cutadapt samtools bowtie2
• 912 views • link
updated by Ram Ram • written by S • S

1 answer

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).

• 0 views • link
written by ATpoint ATpoint

Log in to answer this question.

More posts like this