Actually sequencing primer is designed in such a way that the first base sequenced starts with base 1 of insert. There is an explanation of adapters in this document from Tufts Sequencing core.
Are adapter sequences trimmed from ONLY the 3' ends of reads
Hello everyone!
I learn from this post[1] that Libraries prepared with Illumina library prep kits require adapter trimming only on the 3’ ends of reads, because adapter sequences are not found on the 5’ ends.
However, when we use tools like cutadapt, options are available for removing sequence of an adapter ligated to the 5' end of first or second mate.
It looked confusing to me. Did I make some misunderstanding on this issue?
My guess is that sequencing can also start from the adapter before the first base of the DNA insert in Reads 1 and 2. Am I right?
Thanks!
1 answer
The options for 5' trimming are available because sometimes there may be additional adapters ligated there.
The regular 5' Illumina sequencing adapter is recognized and automatically trimmed by the instrument itself.
• 0 views
•
link
written
by
Istvan Albert
Log in to answer this question.
More posts like this
-
How to figure out adapter sequence to use for trimming old miRNAseq data
written by hsothers •
-
Overrepresented Sequences persistence
written by Luna •
-
Adaptor sequences in GIAB samples
written by Mk •
-
How to remove multiple adapter sequences by Cutadapt
written by okiedokie1208 •
-
How to trim reads when I'm not sure where they are?
written by avelarbio46 •
-
which sequence adapter trimming tool should i use for my illumina 101pb reads ?
written by v.berriosfarias •
-
Variable read length distribution after cutadapt running for my ATAC-seq datasets
written by yaoyao20152031 •
-
problem with some argument in cutadapt
written by zizigolu
-
Remove Illumina Adapters
written by K.Nijbroek •
-
Trimming Adapters
written by newDNASeqer
