Entering edit mode
6.1 years ago
jaqx008
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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)
I think Ion adapters are trimmed by default.
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.
FastQC is great but I find it to under-report adapter contamination, BBDuk is more sensitive in this regard.
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.
I think I understand now and my fastq file seem to already trimmed. Thanks for your suggestions
A link to the data would help.
https://www.ncbi.nlm.nih.gov/sra/SRX2245299[accn]
Does it make sense now? sorry for unclear title
Could you edit the title to something that does make sense?