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miRNA/smallRNA adapter triming: recommendations for adaptor error rate and Q-trim
I am looking for recommendations on how to trim miRNA/smallRNA sequencing data because the trimming may affect the final results (differences are not enormous, but some miRNA are more prone to different parameters in trimming step), but some miRNA are more prone to different parameters in trimming step).
For small RNA seq data trim, I use cutadapt, with minimal sequence length 15, sequence end quality trim Phred20 before adaptor removal and error rate in adaptor detection 0.1 (cutadapt -m 15 -q 20 -e 0.1). The more stringent parameters with (q30 error rate 0.01) give less mature miRNA (logically), but higher differences in DE in downstream analysis.
As I read it is known that miRNA need less stringent parameters for adapter trimming due to more sequencing noise compared to other RNA and DNA seq data.
I would be grateful for sharing your experience.
For small RNA seq data trim, I use cutadapt, with minimal sequence length 15, sequence end quality trim Phred20 before adaptor removal and error rate in adaptor detection 0.1 (cutadapt -m 15 -q 20 -e 0.1). The more stringent parameters with (q30 error rate 0.01) give less mature miRNA (logically), but higher differences in DE in downstream analysis.
As I read it is known that miRNA need less stringent parameters for adapter trimming due to more sequencing noise compared to other RNA and DNA seq data.
I would be grateful for sharing your experience.
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