trimmomatic perform ILLUMINACLIP step, choosing the Adapter sequences

1

Hi when using the function trimmomatic flexible read trimming tool for Ilumina NGS data how do i know which adapter sequence to select for my data
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i am using SRA5395998 for my data set

ive also attatched a screenshot for reference

Image 3-19-23 at 8.56 PM
Image 3-19-23 at 8.56 PM1365×657 189 KB

2

Hi @Preet_Kaur
please consider removing the duplicated post.
Kind regards,
Igor

3

Hi ive edited my post for a new question,
Thanks Igor

4

Hi @Preet_Kaur
your sequencing provider should give you information about kit or protocol used for library preparation. Trimmomatic has built-it option for trimming various illumina adapters. If you have illumina data, just select an appropriate option. For other sequencing platform you need adapter sequences.
Hope that answers the question.
Kind regards,
Igor

5

Hi igor

this is what it says about my SRA
Name: LowO2_Treat_5

Instrument: Illumina HiSeq 1500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: unspecified

Layout: SINGLE

based on this would it be appropriate to select truseq 2 for ilumina GAII?

6

Hi @Preet_Kaur
GAII is a very old machine. Your data was generated on HiSeq.
Maybe check results of FastQC for untrimmed reads. It recognizes adapter sequences.
Kind regards,
Igor