Remove Illumina Adapters
Hi,
I've got mate-paired reads via Illumina HiSeq, and they may contain adapter/primer sequences. Does anyone of you know the best tool which can detect these adapter/primer sequences and remove these from .FASTQ files? Preferable the tool has to work on windows (such as java tools).
I have tried cutadapt but since cutadapt relies on known adapter/primer sequences it won't do the trick (and I didn't manage to get it working on windows).
Thanks,
• 4,491 views
•
link
updated
by
Ram
•
written
by
K.Nijbroek •
•
written
by
K.Nijbroek •
1 answer
Trimmomatic is a good and fast option.
But, every tool will require that you tell it what the adapters are, after all how would these know what to cut off, your samples could have all kinds of systematic sequences in them
• 0 views
•
link
updated
by
Ram
•
written
by
Istvan Albert
•
written
by
Istvan Albert
Log in to answer this question.
More posts like this
-
Identifying primers in rna-seq data
written by mtsrn •
-
What is the relationship between Illumina P5 P7, universal adapters, and TruSeq Adapter Index 7?
written by octpus616 •
-
Removing overrepresented sequences in paired end RNA-seq
written by LayneSadler
-
Adaptor sequences in GIAB samples
written by Mk •
-
Removing Illumina PCR primer sequences from TSA for GenBank upload
written by Michael Dondrup
-
Trimming Overrepresented Sequences in paired-end RNA-Seq data, as underlined by FastQC.
written by Shaurya Jauhari •
-
How to carry out quality control using Trimmomatic on SRA reads of SAGE-RNASeq?
written by hasche89 •
-
Separating mixed bacterial 16S RNA sequences from eukaryotic 18S ITS sequences?
written by Lionel12 •
-
Discard reads with low quality
written by K.Nijbroek •
-
Adapter Clipping
written by Steffi
Just out of curiosity: which tool are you then using to align in windows? If you are using some commercial tool maybe they also perform adapter removal. However, as Istvan Albert pointed out, any tool for removing adapters will require you to know adapter sequences.