Cool tool! Wish I had known about this earlier
• 0 views
•
link
written
by
Michael Dondrup
How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?
Hi all, i want to perform some analysis on small RNA sequence samples retrieved from the Sequence Read Archive (SRA). since adapter contamination is common in small RNA seuquencing results, its important to clip the adapter from the retrieved fastq file before the downstream analysis. to clip the adapter, i need to know its sequence.
so my question is : how do i know what was the adapter used in the sample preparation?
an example experiment : SRAsmallRNA_experiment
• 28,490 views
•
link
updated
by
Alastair Kerr
•
written
by
Doctoroots
•
written
by
Doctoroots
1 answer
Run the sequences through fastQC It will also detect loads of other weirdness as well including both adaptor and primer contamination, quality problems etc. All sequences for the contaminants are present in the config file called "contaminant_list.txt"
• 0 views
•
link
written
by
Alastair Kerr
BBMap suite includes sequences of all popular adapters in a file called "adapters.fa" in resources directory you will find in BBMap folder.
TruSeq is the name of the illumina sequencing protocol, so they are the same. Recent Hiseq and Miseq machines should be covered by TruSeq version3 adapter sequences, at least that is what works with Trimmomatic.
• 1 views
•
link
written
by
Michael Dondrup
Dear Michael
I sent an E-mail to manager of FastQC and ask him about this adapter,ha said The universal adapter isn’t actually an adapter sequence as such, it’s the common sequence which exists at the start of all of the illumina adapter and primer sequences before they diverge into the different sub-variants. This is the first sequence you encounter when you read off the end of an insert on an illumina run so you can use it for detecting and trimming adapters without having to know exactly which one was used.
it is an additional info?
or
It means I should remove 3and 5 terminal nucleotide for trim universal adapter?
You can use that sequence with CLC according to these directions.
Log in to answer this question.
More posts like this
-
Understanding NCBI vs ENA data
written by wes •
-
Per base sequence content error in RNAseq analysis
written by ahmad.sajad4541 •
-
Validate and Trim 3'adapter(P-UCGUAUGCCGUCUUCUGCUUGUidT)
written by Jichen Wen •
-
Small RNA library contaminated by primers?
written by eva.lucarelli •
-
How to find adaptor sequences from SRA sample?
written by akshay_ware •
-
How important is to heat 5' Adapter in Step D of NEXTFLEX Small RNA-Seq Kit for Illumina Platforms?
written by tatisaccon •
-
Trimming Adaptor in Small RNA Analysis
written by ebrahimiet •
-
samll RNA-seq data preproccess （ clipping the adapter sequences, removing reads with Ns)
written by bio_zhangxl •
-
Problems With Analysis Of Small Rnaseq Data - Adapter Trimming
written by Bharat Iyengar
-
Best Reference For Small Rna Alignment And Annotation
written by Doctoroots
Found by google ("illumina adapter sequence"): http://seqanswers.com/forums/showthread.php?t=198
Hi Michael, i know this sequence list, but it seems that sometimes a different adapter is used, or a similar adapter with a few nucleotides difference at the beginning or end. i wanted to know if there is a way to find the exact adapter used. thanks.