How to enter the Adaptor sequence manually？

FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

GNU General Public License v3.0

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How to enter the Adaptor sequence manually？ #100

Closed Rui-Jing closed 4 years ago

Rui-Jing commented 4 years ago

Hi， Thanks for developing this user-friendly tool. I have a problem about remove adaptor from sequencing data. Below is a schematic of my sequencing sample: In the sequencing sequence, the red N on behalf of the DNA sequence, others are adaptor. So, How do I remove these adaptors with trim_galore, manually? Looking forward to your kind reply.

FelixKrueger commented 4 years ago

Hi Rui,

I am currently on holiday and will only be able to take a look at this next week I am afraid. As a first step, I would run your data through FastQC. If you find that FastQC produces a line for Illumina standard adapter (typically in red), then you can just run Trim Galore in default mode (trim_galore --paired file1 file2) as this will just do the right thing. Else, could you attach or email me the FastQC html report to take a look myself? Thanks, Felix