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7.9 years ago
vytarasov
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180
I am programming the function to remove the sequencing adapters from reads. I need to know all these adapters sequences (for 454 and etc). Questions are following. Are all these techniques using always the same predefined set of adapter sequences (each company their own set) or they can be new from time to time ? Is there somewhere the list of used adapters or I have to search each company site to get these sequences?
Any specific reason you are programming your own when there are multiple (commonly used) programs (e.g. BBduk, trimmomatic, cutadapt, skewer etc) available already that do this.
I am just making my own program including this function.
Programs mentioned above include adapter sequence files (BBduk has a comprehensive one that covers many kits). You could adapt/re-use long as you provide appropriate attribution.
I was also thinking to make the identification of adapter by program itself when user provide set of reads. How often companies are changing their adapters?
Companies don't often change the adapters unless perhaps a completely new kit is going to be released. Users on the other hand can do whatever when they design/use custom adapters/primers.
In general the adapters would not be present in the reads (unless the inserts are short e.g. illumina tech) so you would not see them.
I remember that I had to clean the reads from adapters (the company adapters from 454 ) for our miRNA reads.
You are correct. miRNA's are a special case since they are expected to be shorter than 50 bp or so read lengths that are generally used for Illumina. But then you would know that going into the analysis.
If you search for illumina adapter sequences you should be able to find a letter from Illumina that lists the sequences (originally this letter was supposed to be for customers only but there are enough links floating around).
454 adapters can be found in: http://454.com/downloads/my454/documentation/technical-bulletins/TCB-09004_UsingMultiplexIdentifierAdaptorsForTheGSFLXTitaniumSeriesChemistry-BasicMIDSet.pdf
Thanks for the tip !