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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Raw or trimmed data set as input? #94

Closed Silverfoxcome closed 9 months ago

Silverfoxcome commented 5 years ago

Hi! Sometime ago I ran NOVOPlasty using the whole raw dataset because I didn't have enough space to generate datasets with adapters trimmed. Now I have it, so I was wondering if I should ran again NOVOPlasty with the adapters removed like you say in the intructions:

DO NOT filter or quality trim the reads!!! Use the raw whole genome dataset (Only adapters should be removed)!

Thank you in advance for your help!

ndierckx commented 5 years ago

Hi, usually not trimming causes no problem but if evey read has still adapters at the end its best to trim them. Is it assembly with 8 options? And am on holiday do couldn't look at those. With the 8 options you should first look at the orientation of the inverted repeat, so you can exclude some already https://github.com/ndierckx/NOVOPlasty/issues/79

Silverfoxcome commented 5 years ago

Hi! thanks for the quick answer!

I was mistaken and my sequences are already trimmed (the fastqc report shows no adapters or overrepresented sequences).

Please, can you tell me what tools could I use to look at the orientation of the inverted repeats? I'm pretty new to the field of bioinformatics.

I was using Mauve and I got this for the NOVOPlasty run when the output were 8 assemblies: https://cdn1.imggmi.com/uploads/2019/6/26/f14fd20744e00b98db50ae2e578089eb-full.jpg

and this when I changed the max_memory parameter to 20 instead of 15 (and I used the latest version of NOVOPlasty (3.3): https://cdn1.imggmi.com/uploads/2019/6/26/5bbd52d4b1d9d4582b568b6c1e1ee2c8-full.jpg

ndierckx commented 5 years ago

Hi, just got back from holiday. Didn't you check the previous topic I added in the last comment? https://github.com/ndierckx/NOVOPlasty/issues/79