smallRNA - adaptor trimming stringency

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7.8 years ago

ti&te ▴ 40

Dear all,

I am trying to analyze my smallRNA seq data and before alignment it is recommended to trim sequenced reads. What stringency for trimming adaptors do you use in your experiments? I have tried with 0.7 and 0.95 adaptor trimming stringency and I got very different results that differ in proportion of mature RNA and iso-miRNA . Any suggestion?

Thank you for your help...

RNA-Seq adaptors smallRNA trimming stringency • 2.1k views

ADD COMMENT • link updated 7.7 years ago by Biostar 20 • written 7.8 years ago by ti&te ▴ 40

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Please show us what commands did you use and adapter sequences used ? How does the length distribution of reads look after trimming adapters.

ADD REPLY • link 7.8 years ago by Chirag Nepal ★ 2.4k

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We use Basespace trimmer app - FASTQ Toolkit. RNA libraries were prepared using NEB smallRNA library preparation kit, where 3' adaptor sequence is AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and 5' adaptor GTTCAGAGTTCTACAGTCCGACGATC.

Pic of trimmed seq distribution: enter image description here

ADD REPLY • link 7.8 years ago by ti&te ▴ 40

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