Question: How do I find adaptors for my miRNA seq data?
0
gravatar for jaqx008
20 months ago by
jaqx00870
jaqx00870 wrote:

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)

mirna-seq ion torrent • 576 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by jaqx00870
1

I think Ion adapters are trimmed by default.

ADD REPLYlink written 20 months ago by h.mon30k
1

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 REPLYlink modified 20 months ago • written 20 months ago by ATpoint36k

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

ADD REPLYlink written 20 months ago by h.mon30k

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 REPLYlink modified 20 months ago • written 20 months ago by ATpoint36k

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

ADD REPLYlink written 20 months ago by jaqx00870

A link to the data would help.

ADD REPLYlink written 20 months ago by ATpoint36k

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

ADD REPLYlink written 20 months ago by jaqx00870

Does it make sense now? sorry for unclear title

ADD REPLYlink written 20 months ago by jaqx00870

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

ADD REPLYlink modified 20 months ago • written 20 months ago by WouterDeCoster44k
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