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ksahlin / isONcorrect

Error correction of ONT transcript reads
GNU General Public License v3.0
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Transcript quantification #12

Closed kvittingseerup closed 2 years ago

kvittingseerup commented 2 years ago

Hi Kristoffer (great name btw ;) )

Do you know if it is possible to make a reference-free transcript assembly from the output of isOncorrect?

Cheers Kristoffer

ksahlin commented 2 years ago

Hi @kvittingseerup,

Indeed ;)

We are working on it :) Hope to get back to you soon about it.

What we have used up until now is the pipeline isONclust -> isONcorrect -> IsoCon

where we have run IsoCon on each corrected-reads cluster from isONcorrect. We then set the parameter --ignore_ends_len 30 to IsoCon (default 15) to account for larger differences in 3' and 5' ends that what IsoCon was designed for. IsoCon was originally designed for targeted data using start and end primers where the 3' and 5' sites were fairly fixed.

It is definitely not a perfect solution both from an accuracy and a runtime aspect, in large part due to the variability in (ONT) data at 3' and 5' ends. The problem needs a tailored solution.

Best, Kristoffer

kvittingseerup commented 2 years ago

Hi Kristoffer

Thanks for the quick and thorough response!

Impressive work btw!

Cheers Kristoffer