Trim Adaptor - dgaolab/IRFinder GitHub Wiki

Trim adaptor is optional. If you're going to directly apply IRFinder on FASTQ files, IRFinder will automatically trim Illumina universal adaptors as a default mode. In the case that users want to figure out what adaptors were used during library preparation, the following approach can be used:

You may wish to download some sample RNA-Seq files from a public database. eg:

$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR900/SRR900288/SRR900288_1.fastq.gz     
$ wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR900/SRR900288/SRR900288_2.fastq.gz

Adaptor Auto Detection:

In the following case it should indicate successful detection of Illumina standard adaptors: AGATCGGAAG, AGATCGGAAG.

$ bin/AdaptorDetect.pl SRR900288_1.fastq.gz SRR900288_2.fastq.gz

===SUMMARY===  
Standard Illumina TruSeq Adaptor 1 and 2 detected: AGATCGGAAG, AGATCGGAAG

Adaptor Trimming:

Adaptor sequences can be trimmed before FASTQ files are sent to IRFinder. Alternatively, adaptor sequences can be used as a parameter if raw FASTQ files are sent to IRFinder (see next page). IRFinder also comes with a built-in script to trim adaptors. An example to trim the adaptors detected above is shown here:

$ bin/util/trim SRR900288_1.fastq SRR900288_2.fastq \    
  trimmed_SRR900288_1.fastq trimmed_SRR900288_2.fastq \    
  AGATCGGAAG AGATCGGAAG