hello and first questions!

[miguelangel]

Hello there!

I'm starting with my brand new data from Roche's 454 pyrosequencing and I have some questions at this point.

First of all, I am not very confident with my .qual files. I have sequences with bases with no less than q10. Is it allright to start my personal trimming? The people who have run the analysis has also done one before, so I understand that low quality bases have been deleted.

Second question: which freeware can I use to work with my .sff files?

Thanks a lot, I hope this questions are not too stupid and that you won't mind to help me.

Cheers, Miguel Ángel

[rexxi]

Hello there!

I'm starting with my brand new data from Roche's 454 pyrosequencing and I have some questions at this point.

First of all, I am not very confident with my .qual files. I have sequences with bases with no less than q10. Is it allright to start my personal trimming? The people who have run the analysis has also done one before, so I understand that low quality bases have been deleted.

Second question: which freeware can I use to work with my .sff files?

Thanks a lot, I hope this questions are not too stupid and that you won't mind to help me.

Cheers, Miguel Ángel

Hi, your first question is related with the quality standard used in the sequencing, 10 or lower as you told, explains a bad quality read (usually that this number can be 64) , but you have to consider that the quantity of reads makes that this factor cannot be importart some times cause there is another reads that can have a good quality of this section of your sequencing proyect. You must make a reads filtering, using a script as is QCfilter to have the best reads of your sequencing and discard the bad quality reads. The other stepts depend of what are you doing, you would must explain a bit of this (genomics, transciptomics, metagenomics, etc.) to help you a bit more.

The freeware software to make an assembly can be Celera, I've tested this and I have good results (sometimes better than in newbler), MIRA is another software but I didnt use it.

[miguelangel]

Thanks a lot.

I am doing a metagenomics study.

I think I can start with my trimming, because most of the bases have a quality better than q10, so I only have to erase short ones.

I will try the freeware you told me.

Cheers