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radio1988 / OneStopRNAseq

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Adapter trimming #13

Closed ryland-mortlock closed 7 months ago

ryland-mortlock commented 8 months ago

Hi, thanks for developing this wonderful tool. I notice that adapter trimming is performed in the pipeline, as evidenced by the FastQC files of raw fastq files versus trimmed fastq files. However, there is no documentation of this on the About page (https://mccb.umassmed.edu/OneStopRNAseq/about.php), user manual, or "Template of the Method Section". Is the adapter trimming performed using cutadapt? Thanks!

radio1988 commented 7 months ago

Hello Ryland,

You're very welcome!

The trimming was done by trimmomatic.

For PE reads, "v1.23.3/bio/trimmomatic/pe" was used For SE reads, "v1.23.3/bio/trimmomatic/se" was used.

We will update the documentations.

Best, Rui

ryland-mortlock commented 7 months ago

Thanks so much!

radio1988 commented 7 months ago

You're very welcome!