Hi All,
I've just started using Galaxy for RNASeq analysis and I'm at the step where I need to trim adapters using cutadapt. I'm pasting my settings below and would greatly appreciate if someone can have a look and let me know if it's all correct.
The raw data are paired-end reads. Four files. Control_R1, Control_R2, Treated_R1, Treated_R2 The Adapter Sequences are
5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (TruSeq Universal Adapter)
3' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG (TruSeq Adapter, Index 1)
Galaxy Settings Single-end or Paired-end reads? Paired-end reads
FASTQ/A file #1 -> Control_R1, Treated_R1
FASTQ/A file #2 -> Control_R2, Treated_R2
Read1 Options -> 3'(End) Adapters -> Enter Custom Sequence -> GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Read1 Options -> 5'(Front) Adapters -> Enter Custom Sequence -> AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
Read2 Options -> 3'(End) Adapters -> Enter Custom Sequence -> GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Read2 Options -> 5'(Front) Adapters -> Enter Custom Sequence -> AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
Filter Option -> Minimum Length -> 20 Read Modification Option -> Quality Cutoff -> 20
Thanks!
