Preprocessing RNA-seq data with BBDuk

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7.6 years ago

Lucila ▴ 20

Hi all,

I am preprocessing my data with BBDuk and have some doubts regarding adapter-trimming. I want to delete all the sequences of adapters and primers from both ends of my reads. When I run BBDuk with ktrim=r and then the result with ktrim=l, I do not obtain the same result (for example, the number of deleted bases in the final file) than if I run it first with ktrim=l and then ktrim=r.

I would like to know if I am doing something wrong, and which would be the best order to do that.

On the other hand, when I perform the quality trimming I do not add any flag indicating the quality encoding. According to FASTQC analysis, my reads are encoded in Sanger / Illumina 1.9. Does the BBDuk recognises this automatically?

Thank you all in advance.

Lucila.

BBDuk Quality Trimming Adapter Trimming RNA-Seq • 2.5k views

ADD COMMENT • link 7.6 years ago by Lucila ▴ 20

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If your libraries were prepared with standard Illumina kits, you do not need to trim adapters from both sides, only right side of reads will contain adapters. If anything is trimmed on the left side, it is a false positive.

ADD REPLY • link 7.6 years ago by h.mon 35k

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