Ev reads present? - Githubissues

Ceres90 commented 3 months ago

This might not be an issue and more of just a misinterpretation of the tool but when I run piranha , the plate map at the bottom appears to say EV reads present in many of my wells but the table only shows unmapped reads , if there are EV reads should there be at least values under Nonpolioev ? I know these samples have enteroviruses in them so I would expect Non-polio EV to show up

aineniamh commented 3 months ago

Hmm, this doesn't look right- it should only show if there are reads mapped- it could be that the reads do map, but are being filtered out for quality reasons. If piranha is run in no-temp mode, a file is produced that tracks what happens to each read and why it's not included.

I've got a PR that I'm working on that is more permissive of low quality divergent reads, which may resolve this. If you have a small set of reads you'd be happy to share here I can check quickly what the source of this issue is!

Ceres90 commented 3 months ago

demultiplexed.zip

Ceres90 commented 3 months ago

small set attached!

aineniamh commented 3 months ago

Thanks!

Okay, the first thing I realised when running was the default settings in piranha will filter out based on read length, so my first run had removed most of the reads just through read length filtering
I've realised that the colouring on the plot is counting the 'unmapped' read section as well, so the header should really read "Reads present" rather than EV reads specifically, but anything above the minimum read threshold will get flagged as "positive" and you can then filter by specific type with the dropdown menu (e.g. NonPolioEV will show up if it's present).
I changed the filter to allow reads 100bp-1300bp through, and then they were all mostly getting through to the mapping stage, but looking at the minimap2 output, there still was no hits for any of these reads. I played around with the minimap2 settings a bit (we used asm20 currently and I tried out map-ont too) and that didn't change anything. Do you know what enterovirus you're expecting to sequence? It may not be well represented in the default database.

Ceres90 commented 3 months ago

ok that makes sense , I attached a pic of the reads I saw using epi2me

Ceres90 commented 3 months ago

im still relatively new to this , is there a way to check which viruses are included in the default database?

Ceres90 commented 1 month ago

Anyone have a chance to look at why these viruses may not show up on Pirahna?

polio-nanopore / piranha

Ev reads present? #229