Question: How do I find adaptors for my miRNA seq data?
0
gravatar for jaqx008
9 months ago by
jaqx00850
jaqx00850 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 • 387 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by jaqx00850
1

I think Ion adapters are trimmed by default.

ADD REPLYlink written 9 months ago by h.mon27k
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 9 months ago • written 9 months ago by ATpoint21k

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

ADD REPLYlink written 9 months ago by h.mon27k

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 9 months ago • written 9 months ago by ATpoint21k

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

ADD REPLYlink written 9 months ago by jaqx00850

A link to the data would help.

ADD REPLYlink written 9 months ago by ATpoint21k

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

ADD REPLYlink written 9 months ago by jaqx00850

Does it make sense now? sorry for unclear title

ADD REPLYlink written 9 months ago by jaqx00850

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

ADD REPLYlink modified 9 months ago • written 9 months ago by WouterDeCoster40k
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