what is the Hiseq 2000 adaptor sequences

Question

[hana]

Hi

I have some RNA samples(paired-end reads) . The cDNA synthesised by TruSeq RNA sample preparation kit and sequenced by illumina Hiseq 2000 platform .

I would like to use trimmomatic to trim the reads. Can anyone let me know how I can find the adaptor sequence?

Thank you

[hana]

Thank you so much for sharing the information

Answer 1

[GouthamAtla]

1. You will get this information from the sequencing facility from where the data is generated.
2. Run FASTQC and look at the over represented sequences, which may give the name of the adapter sequence. It looks for different adapters which are listed here.
3. Use universal adapter sequences of TruSeq kit: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT

Answer 2

[rtliu]

Personally I would use /Path-To-Trimmomatic-0.33/adapters/TruSeq3-PE-2.fa

It was included in the binary of Trimmomatic.

Answer 3

[Charles Plessy]

Illumina documents adaptor sequences in its "Customer Sequence Letter".

Answer 4

[ewre]

http://supportres.illumina.com/documents/documentation/chemistry_documentation/experiment-design/illumina-customer-sequence-letter.pdf probably has the answer you are looking for.

Sorry, Charles Plessy already give the file I mentioned above, forget about it.