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nanoporetech / tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

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Is there a minimum sequence length/ can resquiggle work with a 38 nt reference?

zaettu opened this issue · comments

commented

Hi
I am interested in comparing the signals for short (20-40 nt) modified oligos.
resquiggle runs error-free and produces the index file, yet it says:

Final unsuccessful reads summary (100.0% reads unsuccessfully processed; 7836 total reads):
100.0% (7836 reads): Alignment not produced

I wonder If the sequence is just too short, to give an alignment with sufficient quality? I can find the reference sequence in the fastq files by text search, so it is definitely there.

Does anyone know about some kind of threshold that prevents the alignment of short sequences?

Thanks for your help!