What do you use to generates summary statistics of sequence and quality data for PacBio?

Question

[Medhat]

Hi,

As it is clear in the title I am new in dealing with PacBio data, The first step that should be done when you have your sequence is to get familiar with the sequence in the case of second generation gene sequencing we may use RINSEQ ,FastQC ...

The question is;

There is another tools to deal with PacBio data?

as for example; PRINSEQ particular designed for 454 /Roche data , so what about PacBio

Thanks

Answer 1

[Biomonika (Noolean)]

I take a look at reports generated by smrtanalysis portal (http://www.pacb.com/devnet/). Then you can check what's the read length distribution, read quality, polymerase quality, length of movie recorded and many others.

FastQC reports on filtered_subreads.fastq will have very poor quality (compared to what you see when looking at Illumina), but that's totally fine. In smrtanalysis portal, you can also set how much you want to filter your sequences if you have raw files - bas.h5 and bax.h5 files.

Pacbio is totally different world, so you need to use different mappers, different assemblers and different strategies to achieve your goals.

[Medhat]

You mean by report here is to use SMRT portal?! as I used it under protocol RS_subread.1 Or shall I use other protocol also do you have any tutorial that I can read to gain more knowledge about How to deal with the data I have?