How do I find adaptors for my miRNA seq data?

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5.5 years ago

jaqx008 ▴ 110

Hello everyone, I downloaded a miRNA-seq data from NCBI and I want to clip the adaptor sequences, but the adaptor sequence used was not included in the experimental description. How do I find the adaptor sequence to usse for clipping the fastq data? the link to the page is https://www.ncbi.nlm.nih.gov/sra/SRX2245299[accn] Thanks (read was single end)

ion torrent miRNA-seq • 1.5k views

ADD COMMENT • link 5.5 years ago by jaqx008 ▴ 110

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I think Ion adapters are trimmed by default.

ADD REPLY • link 5.5 years ago by h.mon 35k

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Would probably agree because I was playing around with the adapter sequences I found on answers but according to fastqc, none of then could be detected.

Here is the file I found.

ADD REPLY • link 5.5 years ago by ATpoint 82k

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FastQC is great but I find it to under-report adapter contamination, BBDuk is more sensitive in this regard.

ADD REPLY • link 5.5 years ago by h.mon 35k

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Also, if you check the sequence length distribution, it strongly peaks at 20-30bp where you expect trimmed miRNA reads rather than untrimmed reads, supporting that reads are already trimmed.

ADD REPLY • link 5.5 years ago by ATpoint 82k

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I think I understand now and my fastq file seem to already trimmed. Thanks for your suggestions

ADD REPLY • link 5.5 years ago by jaqx008 ▴ 110

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A link to the data would help.

ADD REPLY • link 5.5 years ago by ATpoint 82k

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https://www.ncbi.nlm.nih.gov/sra/SRX2245299[accn]

ADD REPLY • link 5.5 years ago by jaqx008 ▴ 110

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Does it make sense now? sorry for unclear title

ADD REPLY • link 5.5 years ago by jaqx008 ▴ 110

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Could you edit the title to something that does make sense?

ADD REPLY • link 5.5 years ago by WouterDeCoster 47k

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