Lexogen Quantseq Mapping Rates with Salmon
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11 weeks ago

Hello!

I have been using Salmon to align QuantSeq reads to the human transcriptome and have been coming up with ~40-60% mapping rates for all of my samples. I have run the reads through quality control for min Phred scores, minimum lengths, and decontamination with no luck at improving the mapping rates. I am very new to using QuantSeq data and am curious if this is typical for human transcriptome alignments, or if these rates are low enough to be worried. Long term, I am hoping to perform differential gene expression on these samples, and want to make sure I am not missing anything with the alignment step.

Thanks for your help!

Abner Apsley

Quantseq RNAseq Salmon Lexogen Mapping • 343 views
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Lexogen Quantseq has specific recommendations on data analysis that can be found here. Are you following those?

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Thanks for the response!

Yes, I have been using these as a template for my aligning (I used Salmon instead of STAR however). In reading this article [1] It looks like they are obtaining around 80% mapping rates with Salmon and QuantSeq. Any suggestions?

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% mapping is a characteristic of quality of your libraries. So you may need to go with what you have on hand. Quantseq is a 3'-end focused library kit so keep that in mind. If you get better results with STAR then you may want to go with that instead.

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Sounds great, I really appreciate the help!

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