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5.4 years ago
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I would like to analyze some small RNA data from NCBI (eg. https://www.ncbi.nlm.nih.gov/sra/SRR5593145), but I am not sure where I can find the adaptor sequences for trimming. Can anyone please suggest.
How Can I Tell What Is The Adapter Used In A Sequence Read Archive (Sra) Sample?
Identify adapter sequences for trimming from Illumina paired end fastq files
Thank you! Not sure if I can use BBMAP if it's single ends though.
TrueSeq small RNA kit sequences (based on the SRA link) should be in their sequence document.
Hi - apologies if I missed the answer somewhere on biostars... so I take it that the
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option infasta-dump
isn’t trimming the adapters? Or cannot be completely trusted?Did never hear of that option, and never heard anyone would use it for adapter trimming. By default NCBI does not store information on the adapter sequence, so not only does the tool not know what to look for, nor would I put any trust in this option. If you do not know the sequence run
fastqc
to check for adapters and then remove with specialized software such astrimmomatic
,cutadapt
orbbduk.sh
. Depends on library prep kit which adapter was used.Thank you ATpoint for the recommendations. Submitters to SRA do generally give information regarding library construction protocol like giving the RNA prep kit they used. The SRA toolkit is honestly quite confusing and I also wonder if ENA is removing these adapters. See below in list of options about
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:ENA mirrows NCBI, they don't change data. You will always have to trim adapters yourself using any (but not exclusively) of the tools I suggested. It is true that the method text may contain infos on library prep but this is just text, there is nothing like a field to enter an adapter sequence. NCBI will always (at least I never saw anything else) raw sequencing data as they came from the sequencer (at least this should be what submitters upload) because everyone should be free to use whatever adapter-removal strategy (or general data manipulation pipeline) they want.