Doesn't match if U nucleotide used in sequence

[keenhl]

If you have an RNA sequence with U's, the U's will have to be converted to T's to get an alignment. Just something users might want to be aware of.

[StevenWingett]

Hi,

Thanks for you message. So far as I am aware, NGS sequencers actually sequence DNA or cDNA (e.g. in RNA-seq experiments). Consequently, FASTQ files will contain A, C, T, G (or N).

Is this some new format I need to be aware of that contains Us?

Thanks,

Steven

[keenhl]

Thanks for the response. I got some fastq files generated from a Nanopore direct sequencing of RNA and there were Us instead of Ts. Not sure if that is the default with this kind of experiment or just something the investigators did in the basecalling step.

[StevenWingett]

Hi,

Thanks for bringing this to my attention. I'll raise an issue for me to look into.

Best, Steven