search

lfaino / LoReAn

Long Reads Annotation pipeline
MIT License
71 stars 10 forks source link

Multiple adapter #6

Closed palfalvi closed 6 years ago

palfalvi commented 6 years ago

Hi @lfaino ,

First of all, thank you for the great pipeline. I would like to install LoReAn in a few days, when our system maintenance is finished and try on our plant genome (~2Gb, with lots of illumina, PacBio and ONT RNA-seq data).

If I understood well, LoReAn will orientate the long reads based on the adapters i feed to it. My question is that, can it work with several adaptors? I have 16 PB cells and 4 ONT FC with same adaptors (SMRTer oligo), and one ONT FC with custom primers. Can I just feed them all the oligos and it will select the best hit or will it cause some problem (e.g. highly extended run time)?

Thanks for your answer in advance!

lfaino commented 6 years ago

Hi, well the way that i configure the adapter analysis should not support multiple adapter. however, i`m working on an improvement. I can come back to you when this is ready. it should take few days and you can help me in testing it.

Cheers Luigi

palfalvi commented 6 years ago

Hi Luigi,

Thanks, sounds great! I am happy if I can help testing or anything!

Best, Gergo

lfaino commented 6 years ago

Hi Gergo, i tried to make the multiple adapter work, but i was not able.

sorry Luigi

palfalvi commented 6 years ago

Hi Luigi,

Thank you for your effort.

Do you think in that case it can work if I clip specific adaptors and go with polyA only? Maybe not that accurate, but could improve. What is your opinion?

Best, Gergo

lfaino commented 6 years ago

Hi Gergo, I made an automatic way of discovering adapters based on: 1) low GC content assuming that the adapter contain part of the poly A 2) this sequence should be highly represented in the reads.

you can run lorean with -a option and see what happens

give a try and please let me know the result

Cheers Luigi