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nanopore-wgs-consortium / NA12878

Data and analysis for NA12878 genome on nanopore
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Nanopore trancsriptome reads on UCSC genome browser #36

Open ljw90607 opened 6 years ago

ljw90607 commented 6 years ago

Hello.

I am currently using cDNA sequencing data, and when I tried to upload reads on ucsc, I found my reads representing the strand information in opposite way (I am very postive that all of the sequeces are showing the opposite direction). I am wondering if there's any specific options or steps needed to process the data.

I have generated my data straight out from the MINion, mapped using minimap2 without any filteirng. So I am wondering if there any filtering steps that you perform that is necessary for nanopore sequencing analysis? I was doing some research as well, but I am also hoping to get methods that you might be using.

Thank you for your time and generous help.

cmdcolin commented 5 years ago

This could possibly be to the TS tag from minimap2, which will represent the strand as the opposite if it is set to '-'

cmdcolin commented 5 years ago

Ref https://github.com/lh3/minimap2/issues/88